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  biotoolsCURIE: biotools:pathway-subtyping
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  confidence_flag: tool
  cost: Free of charge
  credit: []
  description: Disease-agnostic Python framework for discovering molecular subtypes
    using pathway-level analysis and Gaussian mixture model clustering with built-in
    validation gates
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  - note: null
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    - User manual
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  download:
  - note: 'pip install pathway-subtyping

      Or with all extras:

      pip install pathway-subtyping[viz,graph]'
    type: Software package
    url: https://pypi.org/project/pathway-subtyping/
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    operation:
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  homepage_status: 0
  language:
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  lastUpdate: '2026-04-14T00:08:33.020569Z'
  license: MIT
  link:
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  - note: Documentation
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    - Other
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    url: https://codeberg.org/pathways/pathway-subtyping-framework
  maturity: Mature
  name: pathway-subtyping
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  owner: pathways
  publication:
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    metadata: null
    note: 'Title: Pathway-Based Molecular Subtyping Reveals a GABA-Collapsed Autism
      Subgroup and Cross-Disease Convergence with Schizophrenia in Human Cerebral
      Cortex'
    pmcid: null
    pmid: null
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    version: null
  relation: []
  toolType:
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  topic:
  - term: Omics
    uri: http://edamontology.org/topic_3391
  - term: Computational biology
    uri: http://edamontology.org/topic_3307
  - term: Machine learning
    uri: http://edamontology.org/topic_3474
  - term: Biosciences
    uri: http://edamontology.org/topic_4019
  validated: 0
  version:
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  - 0.3.1
  - 0.5.0
- accessibility: Open access
  additionDate: '2019-05-27T16:59:15Z'
  biotoolsCURIE: biotools:SLiM_software
  biotoolsID: SLiM_software
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  confidence_flag: null
  cost: Free of charge
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    gridid: null
    name: Philipp Messer
    note: null
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  description: Evolutionary simulation framework that combines a powerful engine for
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    type:
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  - note: The manual for Eidos, the scripting language used by SLiM
    type:
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    url: http://benhaller.com/slim/Eidos_Manual.pdf
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    type: Source code
    url: http://benhaller.com/slim/SLiM.zip
    version: null
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    note: Run individual-based eco-evolutionary simulations with explicit genetics
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      uri: http://edamontology.org/operation_0230
    - term: DNA substitution modelling
      uri: http://edamontology.org/operation_0550
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      uri: http://edamontology.org/operation_3946
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  homepage_status: 0
  language:
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  lastUpdate: '2026-04-13T17:54:54.015039Z'
  license: GPL-3.0
  link:
  - note: SLiM home page in the Messer Lab website
    type:
    - Software catalogue
    url: https://messerlab.org/slim/
  - note: GitHub repository for SLiM
    type:
    - Repository
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  - note: Discussion forum for SLiM questions
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  name: SLiM
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  otherID: []
  owner: bchaller
  publication:
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    metadata: null
    note: 'B.C. Haller, P.W. Messer. (2019). SLiM 3: Forward genetic simulations beyond
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  - doi: 10.1093/molbev/msy237
    metadata: null
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    metadata: null
    note: B.C. Haller, J. Galloway, J. Kelleher, P.W. Messer, P.L. Ralph. (2019).
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    metadata: null
    note: 'BC Haller, PL Ralph, PW Messer. (2025). SLiM 5: Eco-evolutionary simulations
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  - doi: 10.1086/723601
    metadata: null
    note: 'B.C. Haller, P.W. Messer. (2023). SLiM 4: Multispecies eco-evolutionary
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  toolType:
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  topic:
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  description: Coverage inspector for targeted sequencing QC (hg38)
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    type: Downloads page
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    note: null
    operation:
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  homepage: https://github.com/enes-ak/covsnap
  homepage_status: 0
  language:
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  lastUpdate: '2026-04-13T13:11:19.044465Z'
  license: Other
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    url: https://pypi.org/project/covsnap/
  - note: github repository
    type:
    - Repository
    url: https://github.com/enes-ak/covsnap
  - note: 'Install with: conda install -c bioconda covsnap'
    type:
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  maturity: Emerging
  name: covsnap
  operatingSystem:
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  - Windows
  - Linux
  otherID: []
  owner: enes.ak
  publication: []
  relation: []
  toolType:
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  - Command-line tool
  topic:
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    uri: http://edamontology.org/topic_0080
  - term: Data quality management
    uri: http://edamontology.org/topic_3572
  validated: 0
  version:
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- accessibility: Open access
  additionDate: '2026-04-06T14:44:11.549029Z'
  biotoolsCURIE: biotools:sambo_sequential_model-based_optimization
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  confidence_flag: null
  cost: Free of charge
  credit: []
  description: Sequential and model-based optimization for Python with state-of-the-art
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    type:
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  lastUpdate: '2026-04-06T14:44:11.551236Z'
  license: AGPL-3.0
  link:
  - note: null
    type:
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  - note: null
    type:
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    metadata: null
    note: null
    pmcid: null
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  relation: []
  toolType:
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  topic:
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  - term: Data visualisation
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  - term: Machine learning
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  additionDate: '2026-04-02T11:29:54.022786Z'
  biotoolsCURIE: biotools:pathotypr
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  confidence_flag: null
  cost: Free of charge
  credit:
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    gridid: null
    name: I2SysBio (CSIC - Universitat de València)
    note: null
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    typeEntity: Institute
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    rorid: null
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  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
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    version: null
  - note: null
    type: Source code
    url: https://github.com/PathoGenOmics-Lab/pathotypr
    version: null
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    input:
    - data:
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        uri: http://edamontology.org/data_2044
      format:
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    note: train — Build a Random Forest classifier from labeled genomes.
    operation:
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    output:
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      format:
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  - cmd: null
    input:
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      format:
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    note: predict — Assign lineages to genomes using a pre-trained Random Forest model.
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    - term: Variant classification
      uri: http://edamontology.org/operation_3225
    output:
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    input:
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      format:
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    note: classify — Call known SNP markers in assembled genomes against a user-defined
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    operation:
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    - term: Variant classification
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    output:
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        term: Genotype/phenotype report
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      format:
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  - cmd: null
    input:
    - data:
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      format:
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    note: split-fastq — Alignment-free genotyping directly from raw reads using k-mer
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    operation:
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    output:
    - data:
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      format:
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  - cmd: null
    input:
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    note: match — Find the closest reference genome from a set of references for raw
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    operation:
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    output:
    - data:
        term: Genotype/phenotype report
        uri: http://edamontology.org/data_0920
      format:
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        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:
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    metadata: null
    note: null
    pmcid: null
    pmid: null
    type:
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    version: null
  relation: []
  toolType:
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  topic:
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  - term: Microbiology
    uri: http://edamontology.org/topic_3301
  - term: Genotype and phenotype
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    uri: http://edamontology.org/topic_3474
  validated: 0
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  biotoolsCURIE: biotools:eetl_toolset
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  credit: []
  description: 'Modular toolchain for an extensible and customizable ETL pipeline
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    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.'
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    note: null
    operation:
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    input: []
    note: null
    operation:
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  lastUpdate: '2026-03-31T09:51:42.443383Z'
  license: Apache-2.0
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  otherID: []
  owner: victorsp
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  relation:
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  toolType:
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  topic:
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    uri: http://edamontology.org/topic_3345
  - term: Workflows
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  validated: 0
  version:
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  additionDate: '2026-03-30T13:34:06.425220Z'
  biotoolsCURIE: biotools:autoencoder_rf_tabpfn_for_cross-cancer_metabolomics
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  cost: Free of charge
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  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.
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  - note: null
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    operation:
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  - Python
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  maturity: Emerging
  name: Autoencoder_RF_TabPFN for Cross-Cancer Metabolomics
  operatingSystem: []
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  toolType:
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  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
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  description: Versatile package to perform molecular dynamics, i.e. simulate the
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    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
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    many groups are also using it for research on non-biological systems, e.g. polymers.
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  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: []
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  topic:
  - term: Molecular dynamics
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  validated: 1
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- accessibility: Open access
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    url: https://quac.readthedocs.io/
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  description: Rosalution assists researchers study genetic variation 🧬 in patients
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    metadata: null
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  toolType:
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    note: Head of MODIS team at EMBL Heidelberg
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  description: Lab Integrated Data (LabID) is an open-source web-based platform for
    research data management in life science institutes, featuring sample and dataset
    management, an inventory management system and an electronic lab notebook. LabID
    allows recording extensive experimental information about the provenance of data
    (samples, reagents, instrument, protocols, assay parameters) and is designed to
    help individual scientists, research groups and core facilities better manage,
    annotate and share their research according to FAIR principles.
  documentation:
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    type:
    - General
    url: https://grp-gbcs.embl-community.io/labid-user-docs/
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  language: []
  lastUpdate: '2026-03-26T11:00:14.410278Z'
  license: MIT
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    type:
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  - note: Channel for questions from externals
    type:
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  maturity: Mature
  name: Lab Integrated Data (LabID)
  operatingSystem: []
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  owner: laurent_s._v.
  publication: []
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  toolType:
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  - Command-line tool
  topic:
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    uri: http://edamontology.org/topic_3070
  - term: Data curation and archival
    uri: http://edamontology.org/topic_0219
  - term: FAIR data
    uri: http://edamontology.org/topic_4012
  - term: Workflows
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  - term: Data management
    uri: http://edamontology.org/topic_3071
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2018-12-12T12:35:31Z'
  biotoolsCURIE: biotools:bio.tools
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    url: https://biotools.readthedocs.io/en/latest/contributors.html
  description: The community registry of computational tools and data resources for
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  - note: null
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  - note: null
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  language:
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  - Python
  lastUpdate: '2026-03-25T12:24:23.606945Z'
  license: GPL-3.0
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  owner: jison
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  toolType:
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  topic:
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    uri: http://edamontology.org/topic_0089
  - term: Bioinformatics
    uri: http://edamontology.org/topic_0091
  - term: Data curation and archival
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  - term: Computational biology
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  validated: 1
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  additionDate: '2019-08-26T14:34:55Z'
  biotoolsCURIE: biotools:MINERVA_Platform
  biotoolsID: MINERVA_Platform
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  confidence_flag: null
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  description: 'The MINERVA (Molecular Interaction NEtwoRk VisuAlization) platform
    is a standalone webserver for visualization, exploration and management of molecular
    networks encoded in SBGN-compliant format, including files produced using CellDesigner
    or SBGN editors. Visualization of uploaded networks generated by the platform
    is accessible via a web browser to all viewers with the weblink to the resource.


    The MINERVA Platform is a webservice using the Java Server Faces 2 technology.
    The server side, including data parsing, integration, annotation and verification,
    is implemented in Java. The platform uses the Postgres SQL database for data storage
    and the Hibernate framework as a middle layer between web server and database.
    The user web-interface is generated using React.js. The displayed content is visualized
    by OpenLayers API, dedicated JavaScript and CSS.'
  documentation:
  - note: null
    type:
    - Quick start guide
    - Release notes
    - User manual
    - API documentation
    - Citation instructions
    - Terms of use
    url: https://minerva.uni.lu
  download:
  - note: Installation instructions, including debian package, virtual machine images
      and docker containers.
    type: Other
    url: https://minerva.pages.uni.lu/doc/install/
    version: 13.1.3 - 20.0.3
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  elixirPlatform:
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  elixir_badge: 0
  function:
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    input: []
    note: Visualise systems biology diagrams online, on a standalone web server
    operation:
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      uri: http://edamontology.org/operation_3926
    output: []
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    operation:
    - term: Expression data visualisation
      uri: http://edamontology.org/operation_0571
    output: []
  - cmd: null
    input: []
    note: 'Convert between main systems biology layout formats: CellDeslgners SBML,
      SBML layout+render, SBGN-ML, GPML'
    operation:
    - term: Conversion
      uri: http://edamontology.org/operation_3434
    output: []
  - cmd: null
    input: []
    note: Use MINERVA API to access systems biology formats for modelling
    operation:
    - term: Modelling and simulation
      uri: http://edamontology.org/operation_2426
    output: []
  homepage: https://minerva.uni.lu
  homepage_status: 0
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  lastUpdate: '2026-03-24T15:37:40.163855Z'
  license: AGPL-3.0
  link:
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      stability, API access)
    type:
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    url: https://gitlab.lcsb.uni.lu/minerva/core/
  - note: Issue tracker for core functionalities (data and format handling, service
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    type:
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    type:
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  - note: Issue tracker for frontend functionalities
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  maturity: Mature
  name: The MINERVA Platform
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  owner: mjostaszewski
  publication:
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    metadata: null
    note: null
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    pmid: '28725475'
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    metadata: null
    note: null
    pmcid: PMC6821317
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    type:
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    metadata: null
    note: null
    pmcid: PMC4932659
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    type:
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    pmcid: null
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  - term: Omics
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  - term: Translational medicine
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  - term: Systems biology
    uri: http://edamontology.org/topic_2259
  validated: 0
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  - 18.1.1
  - 19.1.0
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- accessibility: null
  additionDate: '2016-11-28T10:07:16Z'
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  credit:
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    fundrefid: null
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  description: HyPPI classifies a protein-protein complex based on its interaction
    type into permanent, transient, or crystal artifact. Permanent protein-protein
    complexes are only stable in their complexed state. Their subunits would denature
    upon dissociation of the protein-protein complex. Transient protein-protein complexes
    are stable in the complexed as well as in the monomeric form, depending on the
    necessary function of the complex. Crystal artifacts have no biological function
    and are artificially formed during the crystallization process. The discrimination
    is performed using two characteristics of the protein-protein complex, the hydrophobicity
    of the interface (ΔGhydrophobic) and the quotient of interface area ratios (IF-quotient).
    The IF-quotient considers whether the protein-protein interface is symmetric.
  documentation:
  - note: null
    type:
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    note: Probability score for interface classification
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  lastUpdate: '2026-03-24T11:37:08.023561Z'
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  link:
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    type:
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  - note: A web API to run HyPPI calculations for protein structures stored in the
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    type:
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    url: https://proteins.plus/help/ppi_rest
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  - Linux
  - Mac
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  publication:
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  - doi: 10.1093/nar/gkx333
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    type:
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  toolType:
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  topic:
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  - term: Molecular interactions, pathways and networks
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  validated: 1
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- accessibility: null
  additionDate: '2020-06-08T16:00:55Z'
  biotoolsCURIE: biotools:metalizer
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  confidence_flag: tool
  cost: Free of charge
  credit:
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    fundrefid: null
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  description: METALizer predicts the coordination geometry of metal ions in metalloproteins.
    Users can compare potential coordination geometries to those found in the examined
    structure. The predicted coordination geometries and the observed metal interaction
    distances can be interactively compared to statistics calculated based on the
    PDB.
  documentation:
  - note: null
    type:
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  download: []
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  function:
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    note: null
    operation:
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      uri: http://edamontology.org/operation_2480
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    output:
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      format: []
  homepage: https://www.zbh.uni-hamburg.de/en/forschung/amd/software/metalizer.html
  homepage_status: 0
  language: []
  lastUpdate: '2026-03-24T11:36:25.572650Z'
  license: Other
  link:
  - note: A web service to run METALizer calculations for protein structures stored
      in the Protein Data Bank.
    type:
    - Service
    url: https://proteins.plus
  - note: A web API to run METALizer calculations for protein structures stored in
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    type:
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  maturity: Mature
  name: METALizer
  operatingSystem:
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  - Mac
  - Linux
  otherID: []
  owner: ehrt
  publication:
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    metadata: null
    note: null
    pmcid: null
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  relation: []
  toolType:
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  topic:
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  - term: Protein binding sites
    uri: http://edamontology.org/topic_3534
  - term: Sequence sites, features and motifs
    uri: http://edamontology.org/topic_0160
  - term: Protein structure analysis
    uri: http://edamontology.org/topic_2814
  - term: Drug discovery
    uri: http://edamontology.org/topic_3336
  - term: Data mining
    uri: http://edamontology.org/topic_3473
  - term: Bioinformatics
    uri: http://edamontology.org/topic_0091
  - term: Data visualisation
    uri: http://edamontology.org/topic_0092
  - term: Molecular interactions, pathways and networks
    uri: http://edamontology.org/topic_0602
  - term: Protein properties
    uri: http://edamontology.org/topic_0123
  validated: 1
  version: []
- accessibility: null
  additionDate: '2016-11-21T10:33:07Z'
  biotoolsCURIE: biotools:dogsitescorer
  biotoolsID: dogsitescorer
  collectionID:
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  - de.NBI-biodata
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  credit:
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    fundrefid: null
    gridid: null
    name: ProteinsPlus Support
    note: Primary Contact for Web Service Issues
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole:
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    note: null
    orcidid: null
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  description: DoGSiteScorer is a grid-based automated pocket detection and analysis
    tool. It applies a Difference of Gaussian filter to detect potential binding pockets
    and splits them into sub-pockets. The method solely uses the 3D structure of the
    protein. Global properties, describing the size, shape, and chemical features
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  description: Web application and service for visualizing small- to medium-scale
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    note: GRNsight automatically lays out a network graph based on an Excel input
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  description: Open-source software application for creating and solving mathematical
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  - '1.16'
  - '1.17'
  - '1.18'
  - '1.19'
  - '1.20'
  - '1.21'
  - 1.21.1
  - '1.22'
  - 1.22.1
  - '1.23'
  - 1.23.1
- accessibility: Open access
  additionDate: '2017-01-13T13:16:12Z'
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  biotoolsID: samtools
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  - Rare Disease
  - SAMtools
  confidence_flag: null
  cost: Free of charge
  credit:
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    gridid: null
    name: Richard Durbin
    note: null
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    rorid: null
    typeEntity: Person
    typeRole:
    - Contributor
    url: null
  - email: samtools@sanger.ac.uk
    fundrefid: null
    gridid: null
    name: Wellcome Sanger Institute
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    - Primary contact
    url: https://www.sanger.ac.uk/
  - email: null
    fundrefid: null
    gridid: null
    name: Samtools Help mailing list
    note: null
    orcidid: null
    rorid: null
    typeEntity: Project
    typeRole:
    - Support
    url: https://lists.sourceforge.net/lists/listinfo/samtools-help
  description: SAMtools and BCFtools are widely used programs for processing and analysing
    high-throughput sequencing data. They include tools for file format conversion
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  documentation:
  - note: HowTos for samtools
    type:
    - Other
    url: http://www.htslib.org/doc/#howtos
  - note: null
    type:
    - User manual
    url: http://www.htslib.org/doc/#manual-pages
  - note: null
    type:
    - Installation instructions
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      - term: CRAM
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      - term: SAM
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    note: null
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    - term: Visualisation
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    - term: Data filtering
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    - term: Data formatting
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    - term: Data editing
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    - term: Data parsing
      uri: http://edamontology.org/operation_1812
    - term: Data sorting
      uri: http://edamontology.org/operation_3802
    output:
    - data:
        term: Sequence trace
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      format:
      - term: BAM
        uri: http://edamontology.org/format_2572
      - term: CRAM
        uri: http://edamontology.org/format_3462
      - term: SAM
        uri: http://edamontology.org/format_2573
  homepage: http://www.htslib.org/
  homepage_status: 0
  language:
  - C
  lastUpdate: '2026-03-18T17:35:31.864480Z'
  license: MIT
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/samtools/samtools
  - note: null
    type:
    - Mailing list
    url: http://www.htslib.org/support/#lists
  - note: null
    type:
    - Issue tracker
    url: https://github.com/samtools/samtools/issues
  maturity: Mature
  name: SAMtools
  operatingSystem:
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  - Linux
  - Windows
  otherID: []
  owner: awhitwham
  publication:
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    metadata: null
    note: The Sequence Alignment/Map format and SAMtools.
    pmcid: PMC2723002
    pmid: '19505943'
    type:
    - Primary
    version: null
  - doi: 10.1093/gigascience/giab008
    metadata: null
    note: Twelve years of SAMtools and BCFtools.
    pmcid: PMC7931819
    pmid: '33590861'
    type:
    - Primary
    version: null
  - doi: 10.1093/bioinformatics/btr509
    metadata: null
    note: null
    pmcid: PMC3198575
    pmid: '21903627'
    type: []
    version: null
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    type: uses
  toolType:
  - Suite
  - Command-line tool
  topic:
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    uri: http://edamontology.org/topic_0102
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  - term: Sequencing
    uri: http://edamontology.org/topic_3168
  - term: Rare diseases
    uri: http://edamontology.org/topic_3325
  validated: 1
  version:
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  - '1.2'
  - '1.3'
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  - '1.5'
  - '1.6'
  - '1.7'
  - '1.8'
  - '1.9'
  - '1.10'
  - '1.11'
  - '1.12'
  - '1.13'
  - '1.14'
  - '1.15'
  - 1.15.1
  - '1.16'
  - 1.16.1
  - '1.17'
  - '1.18'
  - '1.19'
  - 1.19.1
  - 1.19.2
  - '1.20'
  - '1.21'
  - 1.21.1
  - '1.22'
  - 1.22.1
  - 1.22.2
  - '1.23'
  - 1.23.1
- accessibility: Open access
  additionDate: '2017-08-20T16:07:58Z'
  biotoolsCURIE: biotools:htslib
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  confidence_flag: null
  cost: Free of charge
  credit:
  - email: samtools@sanger.ac.uk
    fundrefid: null
    gridid: null
    name: Wellcome Sanger Institute
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
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    - Primary contact
    url: https://www.sanger.ac.uk/
  - email: null
    fundrefid: null
    gridid: null
    name: Samtools Help mailing list
    note: null
    orcidid: null
    rorid: null
    typeEntity: Project
    typeRole:
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    url: https://lists.sourceforge.net/lists/listinfo/samtools-help
  description: The main purpose of HTSlib is to provide access to genomic information
    files, both alignment data (SAM, BAM, and CRAM formats) and variant data (VCF
    and BCF formats). The library also provides interfaces to access and index genome
    reference data in FASTA format and tab-delimited files with genomic coordinates.
    It is utilized and incorporated into both SAMtools and BCFtools.
  documentation:
  - note: null
    type:
    - User manual
    url: http://www.htslib.org/doc/#manual-pages
  download:
  - note: null
    type: Downloads page
    url: http://www.htslib.org/download/
    version: null
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  function:
  - cmd: null
    input:
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      format:
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      - term: FASTA
        uri: http://edamontology.org/format_1929
      - term: SAM
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      - term: BAM
        uri: http://edamontology.org/format_2572
      - term: FASTQ
        uri: http://edamontology.org/format_1930
    - data:
        term: Sequence variations
        uri: http://edamontology.org/data_3498
      format:
      - term: BCF
        uri: http://edamontology.org/format_3020
      - term: VCF
        uri: http://edamontology.org/format_3016
    note: null
    operation:
    - term: Data handling
      uri: http://edamontology.org/operation_2409
    output:
    - data:
        term: Sequence trace
        uri: http://edamontology.org/data_0924
      format:
      - term: CRAM
        uri: http://edamontology.org/format_3462
      - term: FASTA
        uri: http://edamontology.org/format_1929
      - term: SAM
        uri: http://edamontology.org/format_2573
      - term: BAM
        uri: http://edamontology.org/format_2572
      - term: FASTQ
        uri: http://edamontology.org/format_1930
    - data:
        term: Sequence variations
        uri: http://edamontology.org/data_3498
      format:
      - term: BCF
        uri: http://edamontology.org/format_3020
      - term: VCF
        uri: http://edamontology.org/format_3016
  homepage: http://www.htslib.org/
  homepage_status: 0
  language:
  - C
  lastUpdate: '2026-03-18T17:33:38.200309Z'
  license: MIT
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/samtools/htslib
  - note: null
    type:
    - Mailing list
    url: http://www.htslib.org/support/#lists
  - note: null
    type:
    - Issue tracker
    url: https://github.com/samtools/htslib/issues
  maturity: Mature
  name: HTSlib
  operatingSystem:
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  - Linux
  - Mac
  otherID: []
  owner: awhitwham
  publication:
  - doi: 10.1093/gigascience/giab007
    metadata: null
    note: 'HTSlib: C library for reading/writing high-throughput sequencing data.'
    pmcid: PMC7931820
    pmid: '33594436'
    type:
    - Primary
    version: null
  relation:
  - biotoolsID: samtools
    type: usedBy
  - biotoolsID: bcftools
    type: usedBy
  toolType:
  - Library
  topic:
  - term: Data management
    uri: http://edamontology.org/topic_3071
  validated: 1
  version:
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  - '1.1'
  - '1.2'
  - 1.2.1
  - '1.3'
  - 1.3.1
  - 1.3.2
  - '1.4'
  - 1.4.1
  - '1.5'
  - '1.6'
  - '1.7'
  - '1.8'
  - '1.9'
  - '1.10'
  - 1.10.1
  - 1.10.2
  - '1.11'
  - '1.12'
  - '1.13'
  - '1.14'
  - '1.15'
  - 1.15.1
  - '1.16'
  - '1.17'
  - '1.18'
  - '1.19'
  - '1.20'
  - 1.21.1
  - '1.22'
  - 1.22.1
  - 1.22.2
  - '1.23'
  - 1.23.1
- accessibility: Open access
  additionDate: '2025-07-21T09:43:28.406602Z'
  biotoolsCURIE: biotools:metabolink
  biotoolsID: metabolink
  collectionID: []
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: anamendesml@outlook.com
    fundrefid: null
    gridid: null
    name: Ana Mendes
    note: null
    orcidid: https://orcid.org/0009-0008-5170-0927
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  - email: nils.f@bmb.sdu.dk
    fundrefid: null
    gridid: null
    name: Nils J Færgeman
    note: null
    orcidid: https://orcid.org/0000-0002-9281-5287
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  description: A web application for Streamlined Processing and Analysis of Large-Scale
    Untargeted Metabolomics Data.
  documentation:
  - note: null
    type:
    - User manual
    url: https://github.com/M3Metabolomics/MetaboLink/wiki
  download: []
  editPermission:
    authors: []
    type: private
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  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
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    input:
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      format:
      - term: CSV
        uri: http://edamontology.org/format_3752
    note: null
    operation:
    - term: Imputation
      uri: http://edamontology.org/operation_3557
    - term: Standardisation and normalisation
      uri: http://edamontology.org/operation_3435
    output: []
  homepage: https://computproteomics.bmb.sdu.dk/MetaboLink/
  homepage_status: 0
  language:
  - R
  lastUpdate: '2026-03-17T09:34:45.884481Z'
  license: MIT
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/M3Metabolomics/MetaboLink/
  maturity: Emerging
  name: MetaboLink
  operatingSystem:
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  - Linux
  - Windows
  otherID: []
  owner: Pub2Tools
  publication:
  - doi: 10.1093/bioinformatics/btae459
    metadata: null
    note: null
    pmcid: PMC11269424
    pmid: '39018180'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Web application
  topic:
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    uri: http://edamontology.org/topic_3172
  - term: Lipidomics
    uri: http://edamontology.org/topic_0153
  - term: Workflows
    uri: http://edamontology.org/topic_0769
  validated: 1
  version: []
- accessibility: Open access
  additionDate: '2026-03-17T09:01:01.731320Z'
  biotoolsCURIE: biotools:biogrowth
  biotoolsID: biogrowth
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit: []
  description: Biogrowth provides an interface to the biogrowth package for R. It
    includes functions for describing population growth based on the principles of
    predictive microbiology. It can be used for making predictions (constant or dynamic
    environmental conditions; deterministic or dynamic) or model fitting (primary
    models, one-step primary and secondary models, dynamic models and global models).
    The whole project is Open Accesss.
  documentation: []
  download:
  - note: null
    type: Source code
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    version: null
  editPermission:
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  function: []
  homepage: https://foodlab-upct.shinyapps.io/biogrowth4/
  homepage_status: 0
  language: []
  lastUpdate: '2026-03-17T09:21:11.409928Z'
  license: GPL-3.0-or-later
  link:
  - note: null
    type:
    - Service
    url: https://foodlab-upct.shinyapps.io/biogrowth4/
  - note: null
    type:
    - Repository
    url: https://github.com/albgarre/biogrowth4
  maturity: Mature
  name: biogrowth
  operatingSystem: []
  otherID: []
  owner: albgarre
  publication:
  - doi: 10.18637/jss.v107.i01
    metadata: null
    note: Garre, A., Koomen, J., den Besten, H. M. W., & Zwietering, M. H. (2023).
      Modeling Population Growth in R with the biogrowth Package. Journal of Statistical
      Software, 107(1), 1–51. https://doi.org/10.18637/jss.v107.i01
    pmcid: null
    pmid: null
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Web application
  topic:
  - term: Microbial ecology
    uri: http://edamontology.org/topic_3697
  - term: Microbiology
    uri: http://edamontology.org/topic_3301
  - term: Data visualisation
    uri: http://edamontology.org/topic_0092
  - term: Applied mathematics
    uri: http://edamontology.org/topic_3569
  validated: 0
  version:
  - 1.0.8
- accessibility: Open access
  additionDate: '2026-03-16T11:37:02.408710Z'
  biotoolsCURIE: biotools:Freezing-Point
  biotoolsID: Freezing-Point
  collectionID: []
  confidence_flag: tool
  cost: Free of charge
  credit: []
  description: Freezing-Point is a user-friendly open-source software for the automated
    analysis of freezing behavior in rodents. Based on recorded videos or pose estimation
    files. An adaptive, data-driven algorithm automatically determines freezing detection
    thresholds, reducing subjective bias while preserving user oversight. Freezing-Point
    adopts a user-oriented design centered on a graphical interface that provides
    continuous visual access to original data, processing steps and analysis results.
    This design enables users to inspect, validate or refine results while minimizing
    unnecessary data manipulation.
  documentation:
  - note: null
    type:
    - Quick start guide
    url: https://github.com/gillescourtand/Freezing-Point/blob/main/Doc/User_guide.md
  download:
  - note: null
    type: Binaries
    url: https://github.com/gillescourtand/Freezing-Point/releases
    version: 1.0.2
  editPermission:
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  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
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      uri: http://edamontology.org/operation_3799
    output: []
  - cmd: null
    input: []
    note: null
    operation:
    - term: Visualisation
      uri: http://edamontology.org/operation_0337
    output: []
  - cmd: null
    input: []
    note: null
    operation:
    - term: Optimisation and refinement
      uri: http://edamontology.org/operation_2425
    output: []
  homepage: https://github.com/gillescourtand/Freezing-Point
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-03-16T11:37:02.410724Z'
  license: GPL-3.0
  link: []
  maturity: Mature
  name: Freezing-Point
  operatingSystem:
  - Mac
  - Linux
  - Windows
  otherID: []
  owner: gilles.courtand
  publication: []
  relation: []
  toolType:
  - Desktop application
  topic:
  - term: Neurobiology
    uri: http://edamontology.org/topic_3304
  validated: 0
  version:
  - 1.0.2
- accessibility: Open access
  additionDate: '2017-01-13T13:16:01Z'
  biotoolsCURIE: biotools:quast
  biotoolsID: quast
  collectionID:
  - ONTeater
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: quast.support@cab.spbu.ru
    fundrefid: null
    gridid: null
    name: QUAST Support
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    url: null
  description: "QUAST stands for QUality ASsessment Tool.  \nIt evaluates a quality\
    \ of genome assemblies by computing various metrics and providing nice reports."
  documentation:
  - note: null
    type:
    - General
    url: http://quast.bioinf.spbau.ru/
  download: []
  editPermission:
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    type: group
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  elixir_badge: 0
  function:
  - cmd: quast -ek assembly.fa --out output_prefix
    input:
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        term: Sequence set (nucleic acid)
        uri: http://edamontology.org/data_1234
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: '# Running quast on a eukaryotic genome'
    operation:
    - term: Visualisation
      uri: http://edamontology.org/operation_0337
    - term: Sequence assembly validation
      uri: http://edamontology.org/operation_3180
    output: []
  homepage: http://quast.sourceforge.net/quast
  homepage_status: 0
  language:
  - Perl
  - Python
  - C
  lastUpdate: '2026-03-13T09:39:06.494933Z'
  license: GPL-2.0
  link:
  - note: null
    type:
    - Repository
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  - note: null
    type:
    - Issue tracker
    url: https://github.com/ablab/quast/issues
  maturity: Mature
  name: QUAST
  operatingSystem:
  - Linux
  - Mac
  otherID: []
  owner: seqwiki_import
  publication:
  - doi: 10.1093/bioinformatics/btt086
    metadata:
      abstract: Limitations of genome sequencing techniques have led to dozens of
        assembly algorithms, none of which is perfect. A number of methods for comparing
        assemblers have been developed, but none is yet a recognized benchmark. Further,
        most existing methods for comparing assemblies are only applicable to new
        assemblies of finished genomes; the problem of evaluating assemblies of previously
        unsequenced species has not been adequately considered. Here, we present QUAST
        - a quality assessment tool for evaluating and comparing genome assemblies.
        This tool improves on leading assembly comparison software with new ideas
        and quality metrics. QUAST can evaluate assemblies both with a reference genome,
        as well as without a reference. QUAST produces many reports, summary tables
        and plots to help scientists in their research and in their publications.
        In this study, we used QUAST to compare several genome assemblers on three
        datasets. QUAST tables and plots for all of them are available in the Supplementary
        Material, and interactive versions of these reports are on the QUAST website.
        © 2013 The Author.
      authors:
      - name: Gurevich A.
      - name: Saveliev V.
      - name: Vyahhi N.
      - name: Tesler G.
      citationCount: 6872
      date: '2013-04-15T00:00:00Z'
      journal: Bioinformatics
      title: 'QUAST: Quality assessment tool for genome assemblies'
    note: null
    pmcid: PMC3624806
    pmid: '23422339'
    type: []
    version: null
  relation: []
  toolType:
  - Workflow
  topic:
  - term: Sequence assembly
    uri: http://edamontology.org/topic_0196
  validated: 1
  version:
  - v.5.3.0
- accessibility: Open access
  additionDate: '2025-04-30T10:28:37.002350Z'
  biotoolsCURIE: biotools:eucaim_wizard_tool
  biotoolsID: eucaim_wizard_tool
  collectionID:
  - EUCAIM
  confidence_flag: null
  cost: Free of charge
  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: The EUCAIM Wizard Tool performs an analysis of data re-identification
    risks of imaging and clinical data that follow the EUCAIM CDM. It includes and
    uses an EUCAIM specific configuration of the ARX Data Anonymization Tool (biotools:arx),
    by supporting a wide variety of privacy and risk models as well methods for analyzing
    the usefulness of output data.
  documentation:
  - note: null
    type:
    - User manual
    url: https://docs.google.com/document/d/1pi-7SvDKzVSYS78MhvnBX7PcXF3kZAc6/edit?usp=sharing&ouid=115998150174651530097&rtpof=true&sd=true
  download: []
  editPermission:
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    type: private
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  - term: MRI
    uri: http://edamontology.org/topic_3444
  - term: Machine learning
    uri: http://edamontology.org/topic_3474
  validated: 0
  version:
  - v1.0
- accessibility: Open access
  additionDate: '2016-03-17T13:51:10Z'
  biotoolsCURIE: biotools:webnma
  biotoolsID: webnma
  collectionID:
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  - CBU tools
  - UiB tools
  - ELIXIR-NO
  - ELIXIR-Norway
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: Nathalie.Reuter@uib.no
    fundrefid: null
    gridid: null
    name: Nathalie Reuter
    note: null
    orcidid: https://orcid.org/0000-0002-3649-7675
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    - Developer
    url: http://www.cbu.uib.no/reuter/
  - email: null
    fundrefid: null
    gridid: null
    name: Sandhya P Tiwari
    note: null
    orcidid: https://orcid.org/0000-0002-0747-3826
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Kidane M Tekle
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Tristan Cragnolini
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Svenn H Grindhaug
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Lars Skjærven
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Gisle Salensminde
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Edvin Fuglebakk
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Siv M Hollup
    note: null
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Department of Molecular Biology, University of Bergen, Norway
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Computational Biology Unit, Department of Informatics, University of Bergen,
      Norway
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: UiB
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: null
  description: WEBnm@ provides quick, automated computation and analysis of low-frequency
    normal modes for protein structures.
  documentation:
  - note: null
    type:
    - Quick start guide
    url: http://apps.cbu.uib.no/webnma3/howto/single
  - note: null
    type:
    - FAQ
    url: http://apps.cbu.uib.no/webnma3/qanda
  - note: null
    type:
    - General
    - Citation instructions
    url: http://apps.cbu.uib.no/webnma3/about
  download: []
  editPermission:
    authors:
    - eca008
    - korbinib
    type: group
  elixirCommunity:
  - 3D-BioInfo
  elixirNode:
  - Norway
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Protein structure
        uri: http://edamontology.org/data_1460
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
    note: Constructs elastic network model from alpha carbon coordinates of the protein,
      and computes properties to describe large scale conformations. Computes normal
      modes, fluctuation profiles, inter-residue correlations, conformational overlap
      analysis and vector field representations. Structural amino acid profiles, and
      normal mode characteristics describing protein motion, visualized in plots and
      decorated structure visualizations. White space delimited tabular data for normal
      modes and the provided plots
    operation:
    - term: Structure visualisation
      uri: http://edamontology.org/operation_0570
    - term: Protein flexibility and motion analysis
      uri: http://edamontology.org/operation_0244
    output:
    - data:
        term: Plot
        uri: http://edamontology.org/data_2884
      format:
      - term: PDF
        uri: http://edamontology.org/format_3508
    - data:
        term: Sequence profile
        uri: http://edamontology.org/data_1354
      format:
      - term: Textual format
        uri: http://edamontology.org/format_2330
  - cmd: null
    input:
    - data:
        term: Structure alignment
        uri: http://edamontology.org/data_0886
      format:
      - term: FASTA-like (text)
        uri: http://edamontology.org/format_2200
    - data:
        term: Protein structure
        uri: http://edamontology.org/data_1460
      format:
      - term: PDB
        uri: http://edamontology.org/format_1476
    note: Performs comparative analysis of the normal modes of protein structures.
      Computes the Bhattacharyya Coefficient (BC) and the Root Mean Squared Inner
      Product (RMSIP) of aligned parts of the proteins. Alignment of sets of proteins
      to be compared. Multiple protein structures Heatmaps, dendrograms and structural
      amino acid profiles for visual comparison of structural similarity. White space
      delimited tabular data for the provided plots
    operation:
    - term: Protein structure comparison
      uri: http://edamontology.org/operation_2487
    - term: Visualisation
      uri: http://edamontology.org/operation_0337
    output:
    - data:
        term: Plot
        uri: http://edamontology.org/data_2884
      format:
      - term: PDF
        uri: http://edamontology.org/format_3508
    - data:
        term: Structural profile
        uri: http://edamontology.org/data_0889
      format:
      - term: Textual format
        uri: http://edamontology.org/format_2330
  homepage: http://apps.cbu.uib.no/webnma
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-03-11T08:56:55.566213Z'
  license: GPL-3.0
  link:
  - note: null
    type:
    - Repository
    - Issue tracker
    url: https://github.com/reuter-group/webnma3
  - note: Helpdesk and support for ELIXIR Norway services.
    type:
    - Helpdesk
    url: https://elixir.no/helpdesk
  maturity: Mature
  name: WEBnma
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: UiB
  publication:
  - doi: 10.1186/s12859-014-0427-6
    metadata:
      abstract: 'Background: Normal mode analysis (NMA) using elastic network models
        is a reliable and cost-effective computational method to characterise protein
        flexibility and by extension, their dynamics. Further insight into the dynamics-function
        relationship can be gained by comparing protein motions between protein homologs
        and functional classifications. This can be achieved by comparing normal modes
        obtained from sets of evolutionary related proteins. Results: We have developed
        an automated tool for comparative NMA of a set of pre-aligned protein structures.
        The user can submit a sequence alignment in the FASTA format and the corresponding
        coordinate files in the Protein Data Bank (PDB) format. The computed normalised
        squared atomic fluctuations and atomic deformation energies of the submitted
        structures can be easily compared on graphs provided by the web user interface.
        The web server provides pairwise comparison of the dynamics of all proteins
        included in the submitted set using two measures: the Root Mean Squared Inner
        Product and the Bhattacharyya Coefficient. The Comparative Analysis has been
        implemented on our web server for NMA, WEBnmat, which also provides recently
        upgraded functionality for NMA of single protein structures. This includes
        new visualisations of protein motion, visualisation of inter-residue correlations
        and the analysis of conformational change using the. In addition, programmatic
        access to WEBnmat is now available through a SOAP-based web service. WEBnmat
        is available at. Conclusion: WEBnmat v2.0 is an online tool offering unique
        capability for comparative NMA on multiple protein structures. Along with
        a convenient web interface, powerful computing resources, and several methods
        for mode analyses, WEBnmat facilitates the assessment of protein flexibility
        within protein families and superfamilies. These analyses can give a good
        view of how the structures move and how the flexibility is conserved over
        the different structures.'
      authors:
      - name: Tiwari S.P.
      - name: Fuglebakk E.
      - name: Hollup S.M.
      - name: Skjaerven L.
      - name: Cragnolini T.
      - name: Grindhaug S.H.
      - name: Tekle K.M.
      - name: Reuter N.
      citationCount: 87
      date: '2014-12-30T00:00:00Z'
      journal: BMC Bioinformatics
      title: 'WEBnmat v2.0: Web server and services for comparing protein flexibility'
    note: null
    pmcid: PMC4339738
    pmid: '25547242'
    type:
    - Primary
    version: '2.0'
  - doi: 10.1186/1471-2105-6-52
    metadata:
      abstract: 'Background: Normal mode analysis (NMA) has become the method of choice
        to investigate the slowest motions in macromolecular systems. NMA is especially
        useful for large biomolecular assemblies, such as transmembrane channels or
        virus capsids. NMA relies on the hypothesis that the vibrational normal modes
        having the lowest frequencies (also named soft modes) describe the largest
        movements in a protein and are the ones that are functionally relevant. Results:
        We developed a web-based server to perform normal modes calculations and different
        types of analyses. Starting from a structure file provided by the user in
        the PDB format, the server calculates the normal modes and subsequently offers
        the user a series of automated calculations; normalized squared atomic displacements,
        vector field representation and animation of the first six vibrational modes.
        Each analysis is performed independently from the others and results can be
        visualized using only a web browser. No additional plug-in or software is
        required. For users who would like to analyze the results with their favorite
        software, raw results can also be downloaded. The application is available
        on http://www.bioinfo.no/tools/normalmodes. We present here the underlying
        theory, the application architecture and an illustration of its features using
        a large transmembrane protein as an example. Conclusion: We built an efficient
        and modular web application for normal mode analysis of proteins. Non specialists
        can easily and rapidly evaluate the degree of flexibility of multi-domain
        protein assemblies and characterize the large amplitude movements of their
        domains. © 2005 Hollup et al; licensee BioMed Central Ltd.'
      authors:
      - name: Hollup S.M.
      - name: Salensminde G.
      - name: Reuter N.
      citationCount: 105
      date: '2005-03-11T00:00:00Z'
      journal: BMC Bioinformatics
      title: 'WEBnm@: A web application for normal mode analyses of proteins'
    note: null
    pmcid: PMC1274249
    pmid: '15762993'
    type:
    - Primary
    version: '1.0'
  relation:
  - biotoolsID: numpy
    type: uses
  - biotoolsID: biopython
    type: uses
  - biotoolsID: matplotlib
    type: uses
  - biotoolsID: mustang
    type: uses
  - biotoolsID: dssp
    type: uses
  toolType:
  - Web API
  - Suite
  topic:
  - term: Protein structure analysis
    uri: http://edamontology.org/topic_2814
  - term: Protein folds and structural domains
    uri: http://edamontology.org/topic_0736
  validated: 1
  version:
  - '3.5'
- accessibility: null
  additionDate: '2019-09-27T09:58:46Z'
  biotoolsCURIE: biotools:BioMercator
  biotoolsID: BioMercator
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit: []
  description: BioMercator is a software that provides a complete set of algorithms
    and visualization tool covering all steps required to perform QTL meta-analysis,
    graphical representation of large datasets. User may import sequence and genome
    annotations datasets within the software in order to display functional annotation
    related to QTL and meta-QTL.
  documentation: []
  download:
  - note: null
    type: Binaries
    url: https://sourcesup.renater.fr/frs/?group_id=2301
    version: 4.2.3
  editPermission:
    authors:
    - b.guerra01
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: QTL map
        uri: http://edamontology.org/data_1860
      format:
      - term: XML
        uri: http://edamontology.org/format_2332
      - term: Textual format
        uri: http://edamontology.org/format_2330
    - data:
        term: Genome map
        uri: http://edamontology.org/data_1288
      format:
      - term: GFF3
        uri: http://edamontology.org/format_1975
    note: null
    operation:
    - term: Genetic mapping
      uri: http://edamontology.org/operation_0282
    - term: Physical mapping
      uri: http://edamontology.org/operation_2944
    output: []
  homepage: https://sourcesup.renater.fr/projects/biomercator
  homepage_status: 0
  language:
  - Java
  lastUpdate: '2026-03-11T08:56:54.859634Z'
  license: GPL-3.0
  link: []
  maturity: Mature
  name: BioMercator
  operatingSystem:
  - Linux
  - Windows
  - Mac
  otherID: []
  owner: admin
  publication:
  - doi: 10.1093/bioinformatics/bth230
    metadata:
      abstract: 'Summary: Breeding programs face the challenge of integrating information
        from genomics and from quantitative trait loci (QTL) analysis in order to
        identify genomic sequences controlling the variation of important traits.
        Despite the development of integrative databases, building a consensus map
        of genes, QTL and other loci gathered from multiple maps remains a manual
        and tedious task. Nevertheless, this is a critical step to reveal co-locations
        between genes and QTL. Another important matter is to determine whether QTL
        linked to same traits or related ones is detected in independent experiments
        and located in the same region, and represents a single locus or not. Statistical
        tools such as meta-analysis can be used to answer this question. BioMercator
        has been developed to automate map compilation and QTL meta-analysis, and
        to visualize co-locations between genes and QTL through a graphical interface.
        © Oxford University Press 2004; all rights reserved.'
      authors:
      - name: Arcade A.
      - name: Labourdette A.
      - name: Falque M.
      - name: Mangin B.
      - name: Chardon F.
      - name: Charcosset A.
      - name: Joets J.
      citationCount: 382
      date: '2004-09-22T00:00:00Z'
      journal: Bioinformatics
      title: 'BioMercator: Integrating genetic maps and QTL towards discovery of candidate
        genes'
    note: null
    pmcid: null
    pmid: '15059820'
    type: []
    version: '3'
  relation: []
  toolType:
  - Desktop application
  topic:
  - term: Quantitative genetics
    uri: http://edamontology.org/topic_3055
  - term: Plant biology
    uri: http://edamontology.org/topic_0780
  validated: 1
  version:
  - 4.2.3
- accessibility: Open access
  additionDate: '2025-09-25T00:18:49.762990Z'
  biotoolsCURIE: biotools:sertool
  biotoolsID: sertool
  collectionID: []
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: rennmeng@smail.nju.edu.cn
    fundrefid: null
    gridid: null
    name: Meng Ren
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  description: Detection of Sequence-Enriched Regions (SER) in Proteins and Nucleic
    Acids
  documentation:
  - note: null
    type:
    - User manual
    url: https://www.sertool.net/help
  download:
  - note: null
    type: Downloads page
    url: https://www.sertool.net/resource
    version: 1.0.1
  editPermission:
    authors: []
    type: public
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  elixirNode: []
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  elixir_badge: 0
  function:
  - cmd: python SERtool.py A,C,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y --input test.fasta
      --start 20 --point 18 20 30 50
    input: []
    note: Independent scan for 20 amino acids
    operation:
    - term: Sequence clustering
      uri: http://edamontology.org/operation_0291
    output: []
  - cmd: python SERtool.py D-E --input test.fasta --start 20 --point 18 20 30 50
    input: []
    note: Same class D-E analysis
    operation:
    - term: Sequence clustering
      uri: http://edamontology.org/operation_0291
    output: []
  - cmd: python SERtool.py .S --input test.fasta --start 15 --point 5 10 10 30
    input: []
    note: 'Wildcard: all X-S motifs (e.g., DS, RS)'
    operation:
    - term: Sequence clustering
      uri: http://edamontology.org/operation_0291
    output: []
  homepage: https://github.com/rennmeng/SERtool
  homepage_status: 0
  language:
  - Rust
  - Python
  lastUpdate: '2026-03-11T03:31:16.480486Z'
  license: MIT
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/rennmeng/SERtool
  - note: null
    type:
    - Service
    url: https://www.sertool.net/
  maturity: Legacy
  name: SERtool
  operatingSystem:
  - Linux
  otherID: []
  owner: rennmeng
  publication: []
  relation: []
  toolType:
  - Bioinformatics portal
  - Web service
  - Command-line tool
  topic:
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  - term: Sequence sites, features and motifs
    uri: http://edamontology.org/topic_0160
  validated: 0
  version:
  - 1.0.1
- accessibility: Open access
  additionDate: '2026-03-10T17:31:04.487598Z'
  biotoolsCURIE: biotools:rmsx_and_flipbook
  biotoolsID: rmsx_and_flipbook
  collectionID: []
  confidence_flag: tool
  cost: Free of charge
  credit: []
  description: RMSX + Flipbook is a molecular dynamics analysis and visualization
    tool for generating residue-resolved structural motion summaries from simulation
    trajectories. It computes per-residue motion metrics and produces color- and thickness-encoded
    protein snapshots arranged as static flipbook panels or interactive displays for
    publication, presentation, and exploratory analysis.
  documentation: []
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: run_rmsx_flipbook
    input:
    - data:
        term: Trajectory data
        uri: http://edamontology.org/data_3870
      format: []
    note: null
    operation:
    - term: Trajectory visualization
      uri: http://edamontology.org/operation_3890
    output:
    - data:
        term: Image
        uri: http://edamontology.org/data_2968
      format: []
  homepage: https://github.com/AntunesLab/rmsx
  homepage_status: 0
  language:
  - R
  - Python
  lastUpdate: '2026-03-10T17:31:17.950095Z'
  license: MIT
  link: []
  maturity: null
  name: RMSX and Flipbook
  operatingSystem:
  - Mac
  - Linux
  - Windows
  otherID: []
  owner: FinnB
  publication:
  - doi: 10.1038/s41598-026-39869-7
    metadata: null
    note: null
    pmcid: null
    pmid: '41720904'
    type:
    - Primary
    version: null
  relation:
  - biotoolsID: chimerax
    type: uses
  - biotoolsID: mdanalysis
    type: uses
  toolType:
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  - Workflow
  topic:
  - term: Biophysics
    uri: http://edamontology.org/topic_3306
  - term: Computational biology
    uri: http://edamontology.org/topic_3307
  - term: Computational chemistry
    uri: http://edamontology.org/topic_3332
  - term: Molecular dynamics
    uri: http://edamontology.org/topic_0176
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2026-02-22T14:20:37.167505Z'
  biotoolsCURIE: biotools:mapler
  biotoolsID: mapler
  collectionID: []
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: nicolas.maurice@inria.fr
    fundrefid: null
    gridid: null
    name: Nicolas Maurice
    note: null
    orcidid: https://orcid.org/0009-0009-9615-2765
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Claire Lemaitre
    note: null
    orcidid: https://orcid.org/0000-0001-8675-170X
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Riccardo Vicedomini
    note: null
    orcidid: https://orcid.org/0000-0002-7706-0998
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  - email: clemence.frioux@inria.fr
    fundrefid: null
    gridid: null
    name: Clémence Frioux
    note: null
    orcidid: https://orcid.org/0000-0003-2114-0697
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  description: Mapler is a pipeline for assessing assembly quality in taxonomically
    rich metagenomes sequenced with HiFi reads. It incorporates state-of-the-art metrics
    and facilitates the comparison of assembly strategies.
  documentation: []
  download: []
  editPermission:
    authors: []
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  elixirNode: []
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  elixir_badge: 0
  function:
  - cmd: null
    input:
    - data:
        term: Sequence trace
        uri: http://edamontology.org/data_0924
      format:
      - term: FASTQ
        uri: http://edamontology.org/format_1930
    note: null
    operation:
    - term: Sequence assembly
      uri: http://edamontology.org/operation_0310
    output:
    - data:
        term: Sequence set (nucleic acid)
        uri: http://edamontology.org/data_1234
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
  - cmd: null
    input:
    - data:
        term: Sequence set (nucleic acid)
        uri: http://edamontology.org/data_1234
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: null
    operation:
    - term: Sequence assembly validation
      uri: http://edamontology.org/operation_3180
    - term: Sample comparison
      uri: http://edamontology.org/operation_3731
    output:
    - data:
        term: Quality control report
        uri: http://edamontology.org/data_3914
      format:
      - term: DSV
        uri: http://edamontology.org/format_3751
      - term: Textual format
        uri: http://edamontology.org/format_2330
      - term: HTML
        uri: http://edamontology.org/format_2331
  - cmd: null
    input:
    - data:
        term: Sequence set (nucleic acid)
        uri: http://edamontology.org/data_1234
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
    note: null
    operation:
    - term: Read binning
      uri: http://edamontology.org/operation_3798
    output:
    - data:
        term: Sequence set (nucleic acid)
        uri: http://edamontology.org/data_1234
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
  homepage: https://github.com/Nimauric/Mapler
  homepage_status: 0
  language:
  - Bash
  - Python
  lastUpdate: '2026-03-10T15:44:03.311515Z'
  license: AGPL-3.0
  link:
  - note: null
    type:
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    url: https://github.com/Nimauric/Mapler
  maturity: null
  name: Mapler
  operatingSystem: []
  otherID: []
  owner: nimauric
  publication:
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    metadata: null
    note: null
    pmcid: PMC12205171
    pmid: '40478660'
    type: []
    version: null
  relation: []
  toolType:
  - Workflow
  - Command-line tool
  topic:
  - term: Metagenomics
    uri: http://edamontology.org/topic_3174
  - term: Sequence assembly
    uri: http://edamontology.org/topic_0196
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2026-03-06T16:07:44.924976Z'
  biotoolsCURIE: biotools:histoatlas
  biotoolsID: histoatlas
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit: []
  description: A pan-cancer morphology atlas linking histological features to molecular
    and clinical outcomes
  documentation:
  - note: Methodology
    type:
    - General
    url: https://histoatlas.com/methods/
  download: []
  editPermission:
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  elixir_badge: 0
  function:
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    input: []
    note: null
    operation:
    - term: Gene-set enrichment analysis
      uri: http://edamontology.org/operation_2436
    output: []
  homepage: https://histoatlas.com
  homepage_status: 0
  language: []
  lastUpdate: '2026-03-06T16:13:40.932753Z'
  license: CC-BY-NC-4.0
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/HistoAtlas/HistoAtlas
  maturity: null
  name: HistoAtlas
  operatingSystem: []
  otherID: []
  owner: PABannier
  publication: []
  relation: []
  toolType:
  - Web application
  - Bioinformatics portal
  - Database portal
  topic:
  - term: Bioinformatics
    uri: http://edamontology.org/topic_0091
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2026-03-06T01:46:30.618295Z'
  biotoolsCURIE: biotools:STaBioM-stabiom-standardised-bioinformatics-for-microbial-samples
  biotoolsID: STaBioM-stabiom-standardised-bioinformatics-for-microbial-samples
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit: []
  description: A unified CLI + GUI for running microbiome analysis pipelines on long-read
    and short-read sequencing data, supporting both 16S amplicon and shotgun metagenomics
    workflows for all DNA sequencing technologies.
  documentation:
  - note: null
    type:
    - General
    url: https://github.com/izzydavidson/STaBioM-Standardised-Bioinformatics-for-Microbial-samples.git
  download:
  - note: Download whole repo to allow for both CLI and GUI usage
    type: Source code
    url: https://github.com/izzydavidson/STaBioM-Standardised-Bioinformatics-for-Microbial-samples.git
    version: V1
  editPermission:
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  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Taxonomic classification
      uri: http://edamontology.org/operation_3460
    output:
    - data:
        term: Alpha diversity data
        uri: http://edamontology.org/data_3737
      format: []
    - data:
        term: Beta diversity data
        uri: http://edamontology.org/data_3738
      format: []
    - data:
        term: Heat map
        uri: http://edamontology.org/data_1636
      format: []
    - data:
        term: Quality control report
        uri: http://edamontology.org/data_3914
      format: []
  homepage: https://github.com/izzydavidson/STaBioM-Standardised-Bioinformatics-for-Microbial-samples.git
  homepage_status: 0
  language:
  - Shell
  - Python
  - R
  lastUpdate: '2026-03-06T01:59:44.842634Z'
  license: Freeware
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/izzydavidson/STaBioM-Standardised-Bioinformatics-for-Microbial-samples.git
  maturity: Emerging
  name: STaBioM-Standardised-Bioinformatics-for-Microbial-samples
  operatingSystem:
  - Mac
  - Linux
  - Windows
  otherID: []
  owner: izzy_davo
  publication: []
  relation: []
  toolType:
  - Web application
  - Command-line tool
  topic:
  - term: Whole genome sequencing
    uri: http://edamontology.org/topic_3673
  - term: Whole genome sequencing
    uri: http://edamontology.org/topic_3673
  validated: 0
  version:
  - betav1
- accessibility: Open access
  additionDate: '2026-03-05T08:10:23.201211Z'
  biotoolsCURIE: biotools:splithalfr
  biotoolsID: splithalfr
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: t.pronk1@amsterdamumc.nl
    fundrefid: null
    gridid: null
    name: Thomas Pronk
    note: null
    orcidid: https://orcid.org/0000-0001-9334-7190
    rorid: null
    typeEntity: Person
    typeRole: []
    url: null
  description: Estimates split-half reliabilities for scoring algorithms of cognitive
    tasks and questionnaires
  documentation:
  - note: null
    type:
    - Quick start guide
    url: https://github.com/tpronk/splithalfr/blob/main/README.md
  download:
  - note: null
    type: Software package
    url: https://cran.r-project.org/package=splithalfr
    version: null
  editPermission:
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  elixir_badge: 0
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  homepage: https://github.com/tpronk/splithalfr
  homepage_status: 0
  language:
  - R
  lastUpdate: '2026-03-05T08:17:29.680941Z'
  license: LGPL-3.0-or-later
  link:
  - note: null
    type:
    - Repository
    url: https://github.com/tpronk/splithalfr
  maturity: Mature
  name: splithalfr
  operatingSystem: []
  otherID: []
  owner: tpronk
  publication:
  - doi: 10.3758/s13423-021-01948-3
    metadata: null
    note: null
    pmcid: PMC8858277
    pmid: '34100223'
    type:
    - Primary
    version: null
  relation: []
  toolType:
  - Library
  topic:
  - term: Topic
    uri: http://edamontology.org/topic_0003
  validated: 0
  version: []
- accessibility: null
  additionDate: '2026-02-27T17:39:14.144907Z'
  biotoolsCURIE: biotools:random_number_lab
  biotoolsID: random_number_lab
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: hello@randomnumberlab.org
    fundrefid: null
    gridid: null
    name: Thomas Amthor
    note: null
    orcidid: https://orcid.org/0000-0002-1456-6131
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    - Maintainer
    url: null
  description: An interactive set of tools including randomization of data (even stratified
    random sampling) and random assignments for studies, generation of random numbers
    following specific probability distributions, generation of random and quasi-random
    point distributions and sampling patterns, noise in one or two dimensions with
    adjustable spectral properties, random walks and Lévy flights. Own data tables
    can be provided for random sampling in a privacy-friendly way, as data processing
    takes place directly in the browser and no data is transferred to anywhere else.
    The Random Number Lab also offers some educational material and worksheets and
    can be used for scientific and educational purposes.
  documentation: []
  download: []
  editPermission:
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    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: Generation of sequences of random numbers or elements, spatial point patterns,
      random walks
    operation:
    - term: Random sequence generation
      uri: http://edamontology.org/operation_0364
    output: []
  - cmd: null
    input: []
    note: Visualization of random distributions and random processes
    operation:
    - term: Visualisation
      uri: http://edamontology.org/operation_0337
    output: []
  - cmd: null
    input: []
    note: Randomization and permutation of data in a privacy-preserving way
    operation:
    - term: Data handling
      uri: http://edamontology.org/operation_2409
    output: []
  homepage: https://randomnumberlab.org
  homepage_status: 0
  language:
  - JavaScript
  lastUpdate: '2026-02-27T18:10:10.460700Z'
  license: null
  link: []
  maturity: Mature
  name: Random Number Lab
  operatingSystem:
  - Linux
  - iOS
  - Mac
  - Android
  - Windows
  otherID:
  - type: rrid
    value: RRID:SCR_028010
    version: null
  owner: thomas9
  publication: []
  relation: []
  toolType:
  - Web application
  topic:
  - term: Statistics and probability
    uri: http://edamontology.org/topic_2269
  - term: Experimental design and studies
    uri: http://edamontology.org/topic_3678
  validated: 0
  version: []
- accessibility: Open access
  additionDate: '2021-05-06T06:18:52Z'
  biotoolsCURIE: biotools:pangenome-blast
  biotoolsID: pangenome-blast
  collectionID: []
  confidence_flag: null
  cost: Free of charge
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: Bielefeld University
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: https://www.uni-bielefeld.de/
  - email: null
    fundrefid: null
    gridid: null
    name: Genome Informatics
    note: null
    orcidid: null
    rorid: null
    typeEntity: Institute
    typeRole:
    - Provider
    url: https://gi.cebitec.uni-bielefeld.de/
  - email: plast-service@cebitec.uni-bielefeld.de
    fundrefid: null
    gridid: null
    name: Tizian Schulz
    note: null
    orcidid: https://orcid.org/0000-0003-0744-7078
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: null
  description: PLAST is a heuristical method to search for highest scoring local alignments
    between a DNA sequence query and a graphical pangenome. It takes as input a plain
    DNA sequence and a pangenome which may either be a set of (multiple) FASTA or
    FASTQ files or a sequence graph constructed by the tool Bifrost. It then outputs
    statistically meaningful (gapped) alignments in the style of the NCBI BLAST standard
    output format. Alignments are calculated based on a "seed-and-extend approach"
    while traversing the sequence graph. Biologically meaningful alignments are filtered
    by using an alignment statistic explicitly developed for sequence-to-graph alignments
    involving graphical pangenomes.
  documentation:
  - note: null
    type:
    - General
    url: https://gitlab.ub.uni-bielefeld.de/gi/plast/-/blob/master/README.md
  download: []
  editPermission:
    authors: []
    type: private
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: PLAST Search -i pangenomeGraphCommonFilePrefix -q fileContainingOneQueryPerLine
    input:
    - data:
        term: DNA sequence
        uri: http://edamontology.org/data_3494
      format:
      - term: unambiguous pure nucleotide
        uri: http://edamontology.org/format_1211
    - data:
        term: Sequence set (nucleic acid)
        uri: http://edamontology.org/data_1234
      format:
      - term: GFA 1
        uri: http://edamontology.org/format_3975
      - term: Binary format
        uri: http://edamontology.org/format_2333
    note: "In order to search for alignments within the pangenome graph, \nA pangenome\
      \ graph used to search for alignments consists of (1) a file in GFA format containing\
      \ all sequences of the graph, (2) a binary file produced by the tool itself\
      \ or the software \"Bifrost\" and (3) a program-specific index data structure\
      \ in binary format."
    operation:
    - term: Local alignment
      uri: http://edamontology.org/operation_0495
    output:
    - data:
        term: Nucleic acid sequence alignment
        uri: http://edamontology.org/data_1383
      format:
      - term: BLAST results
        uri: http://edamontology.org/format_1333
  - cmd: PLAST Build -i pangenomeGraphCommonFilePrefix -R *.fasta
    input:
    - data:
        term: Sequence set
        uri: http://edamontology.org/data_0850
      format:
      - term: FASTA
        uri: http://edamontology.org/format_1929
      - term: FASTQ
        uri: http://edamontology.org/format_1930
    note: If a pangenome graph already exists and only an index has to be built, FASTA/FASTQ
      files are not needed.
    operation:
    - term: Indexing
      uri: http://edamontology.org/operation_0227
    output:
    - data:
        term: Sequence set
        uri: http://edamontology.org/data_0850
      format:
      - term: GFA 1
        uri: http://edamontology.org/format_3975
      - term: Binary format
        uri: http://edamontology.org/format_2333
  homepage: https://github.com/tischulz1/plast
  homepage_status: 0
  language:
  - C++
  lastUpdate: '2026-02-26T11:22:02.485629Z'
  license: GPL-3.0
  link:
  - note: null
    type:
    - Repository
    url: https://gitlab.ub.uni-bielefeld.de/gi/plast
  - note: null
    type:
    - Mirror
    url: https://github.com/tischulz1/plast
  maturity: Mature
  name: PLAST
  operatingSystem:
  - Linux
  - Mac
  - Windows
  otherID: []
  owner: tizian
  publication:
  - doi: 10.1093/bioinformatics/btab077
    metadata:
      abstract: 'Motivation: Increasing amounts of individual genomes sequenced per
        species motivate the usage of pangenomic approaches. Pangenomes may be represented
        as graphical structures, e.g. compacted colored de Bruijn graphs, which offer
        a low memory usage and facilitate reference-free sequence comparisons. While
        sequence-to-graph mapping to graphical pangenomes has been studied for some
        time, no local alignment search tool in the vein of BLAST has been proposed
        yet. Results: We present a new heuristic method to find maximum scoring local
        alignments of a DNA query sequence to a pangenome represented as a compacted
        colored de Bruijn graph. Our approach additionally allows a comparison of
        similarity among sequences within the pangenome. We show that local alignment
        scores follow an exponential-tail distribution similar to BLAST scores, and
        we discuss how to estimate its parameters to separate local alignments representing
        sequence homology from spurious findings. An implementation of our method
        is presented, and its performance and usability are shown. Our approach scales
        sublinearly in running time and memory usage with respect to the number of
        genomes under consideration. This is an advantage over classical methods that
        do not make use of sequence similarity within the pangenome.'
      authors:
      - name: Schulz T.
      - name: Wittler R.
      - name: Rahmann S.
      - name: Hach F.
      - name: Stoye J.
      citationCount: 6
      date: '2021-08-15T00:00:00Z'
      journal: Bioinformatics
      title: Detecting high-scoring local alignments in pangenome graphs
    note: null
    pmcid: PMC8388040
    pmid: '33532821'
    type:
    - Primary
    - Method
    - Benchmarking study
    version: null
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Comparative genomics
    uri: http://edamontology.org/topic_0797
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  validated: 0
  version:
  - 0.0.1-0.2.0
- accessibility: Open access
  additionDate: '2025-06-25T13:31:29.384393Z'
  biotoolsCURIE: biotools:fantasiav2
  biotoolsID: fantasiav2
  collectionID: []
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: fmpercan@upo.es
    fundrefid: null
    gridid: null
    name: Francisco Miguel Pérez Canales
    note: Programmer
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    - Developer
    - Documentor
    - Maintainer
    - Support
    - Provider
    url: http://www.bioinfocb.es/
  - email: a.rojas.m@csic.es
    fundrefid: null
    gridid: null
    name: Ana M Rojas Mendoza
    note: Scientific concept and functionalities
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Primary contact
    - Contributor
    - Documentor
    - Support
    url: http://www.bioinfocb.es/
  - email: rosa.fernandez@ibe.upf-csic.es
    fundrefid: null
    gridid: null
    name: Rosa Fernandez
    note: Scientific concept and functionalities
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole:
    - Contributor
    - Documentor
    url: https://www.metazomics.com/
  - email: fraruimot@alum.us.es
    fundrefid: null
    gridid: null
    name: Francisco J. Ruiz Mota
    note: Junior developer
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    url: http://www.bioinfocb.es/
  - email: gemma.martinez@ibe.upf-csic.es
    fundrefid: null
    gridid: null
    name: Gemma Martinez Redondo
    note: Contributed  as developer of the first version of FANTASIA V1
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Contributor
    - Developer
    url: https://www.metazomics.com/
  - email: adomrod4@upo.es
    fundrefid: null
    gridid: null
    name: Alex Dominguez Rodriguez
    note: Implemented the LITE version of FANTASIA
    orcidid: null
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    - Primary contact
    - Maintainer
    - Documentor
    url: http://www.bioinfocb.es/
  description: FANTASIA (Functional ANnoTAtion based on embedding space SImilArity)
    is a pipeline for protein annotating via GO term transference using the embedding
    space. FANTASIA’s latest developments include additional protein language models
    and provide enhanced functionalities.
  documentation:
  - note: Full documetnation with user cases, benchmarking, and cluster implementations
    type:
    - General
    url: https://fantasia.readthedocs.io/en/latest/
  download: []
  editPermission:
    authors: []
    type: group
  elixirCommunity:
  - 3D-BioInfo
  - Proteomics
  elixirNode:
  - Spain
  elixirPlatform:
  - Tools
  elixir_badge: 0
  function:
  - cmd: null
    input: []
    note: null
    operation:
    - term: Gene functional annotation
      uri: http://edamontology.org/operation_3672
    output: []
  homepage: https://github.com/CBBIO/
  homepage_status: 0
  language:
  - Python
  - SQL
  lastUpdate: '2026-02-22T21:19:22.986918Z'
  license: MIT
  link:
  - note: Main repository contains documentation  from latest version
    type:
    - Repository
    url: https://github.com/CBBIO/FANTASIA
  - note: Main repository contains documentation  from linitial version based on Bioembeddings
      implementation.
    type:
    - Repository
    url: https://github.com/MetazoaPhylogenomicsLab/FANTASIA
  - note: Recommended tool for the Earth Biogenome Project
    type:
    - Software catalogue
    url: https://www.earthbiogenome.org/report-on-annotation-recommended-tools
  - note: This is the LITE version of FANTASIA for a quick and custom annotation
    type:
    - Software catalogue
    url: https://github.com/CBBIO/FANTASIA-Lite
  - note: This is a repository for FANTASIA-LITE available in Elixir France
    type:
    - Repository
    url: https://gitlab.com/ifb-elixirfr/cluster/tools/-/tree/master/tools/fantasia/0.1.0?ref_type=heads
  maturity: Mature
  name: FANTASIA
  operatingSystem:
  - Linux
  otherID: []
  owner: arojas
  publication:
  - doi: 10.1093/nargab/lqae078
    metadata: null
    note: null
    pmcid: null
    pmid: null
    type:
    - Usage
    version: null
  - doi: 10.1007/978-1-0716-4623-6_8
    metadata: null
    note: This protocol describes the use of the first version of FANTASIA
    pmcid: null
    pmid: '40601255'
    type:
    - Method
    version: 2.8.0
  - doi: 10.1038/s42003-025-08651-2
    metadata: null
    note: Application of FANTASIA to annotate 24 million of genes of 1000 animal species
    pmcid: PMC12354702
    pmid: '40813894'
    type:
    - Primary
    version: '4.0'
  relation: []
  toolType:
  - Command-line tool
  topic:
  - term: Molecular evolution
    uri: http://edamontology.org/topic_3945
  - term: Natural language processing
    uri: http://edamontology.org/topic_0218
  - term: Functional genomics
    uri: http://edamontology.org/topic_0085
  - term: Open science
    uri: http://edamontology.org/topic_4010
  validated: 0
  version:
  - '4.0'
  - LITE
- accessibility: Open access
  additionDate: '2026-02-19T07:51:45.702608Z'
  biotoolsCURIE: biotools:poly_pipeline
  biotoolsID: poly_pipeline
  collectionID: []
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: pccrvl@gmail.com
    fundrefid: null
    gridid: null
    name: Pedro Cristovão Carvalho
    note: Main developer of the pipeline
    orcidid: https://orcid.org/0000-0001-9242-6911
    rorid: null
    typeEntity: Person
    typeRole:
    - Developer
    - Primary contact
    - Maintainer
    - Provider
    - Support
    url: https://cafinvest.com.br/resume.php
  description: A data analysis pipeline for Spatial Transcriptomics data tailored
    to polyploid organisms.
  documentation:
  - note: Github Documentation
    type:
    - User manual
    url: https://github.com/capuccino26/POLY_PIPELINE#poly_pipeline
  download:
  - note: Github Release
    type: Source code
    url: https://github.com/capuccino26/POLY_PIPELINE/releases/tag/v1.0.0
    version: v1.0.0
  editPermission:
    authors: []
    type: private
  elixirCommunity:
  - Plant Sciences
  elixirNode: []
  elixirPlatform:
  - Tools
  elixir_badge: 0
  function:
  - cmd: ANALYSIS=1
    input:
    - data:
        term: Count matrix
        uri: http://edamontology.org/data_3917
      format: []
    note: Clustering of GEF files.
    operation:
    - term: Expression profile clustering
      uri: http://edamontology.org/operation_0313
    output:
    - data:
        term: Clustered expression profiles
        uri: http://edamontology.org/data_3768
      format: []
  - cmd: ANALYSIS=3
    input:
    - data:
        term: Count matrix
        uri: http://edamontology.org/data_3917
      format: []
    note: Generation of Nodes and Edges.
    operation:
    - term: Network visualisation
      uri: http://edamontology.org/operation_3925
    output:
    - data:
        term: Pathway or network
        uri: http://edamontology.org/data_2600
      format: []
  - cmd: ANALYSIS=0
    input:
    - data:
        term: Gene expression matrix
        uri: http://edamontology.org/data_3112
      format: []
    note: Data converter.
    operation:
    - term: Format validation
      uri: http://edamontology.org/operation_0336
    output:
    - data:
        term: Gene expression matrix
        uri: http://edamontology.org/data_3112
      format: []
  - cmd: ANALYSIS=1
    input:
    - data:
        term: Gene expression matrix
        uri: http://edamontology.org/data_3112
      format: []
    note: Generation of count matrix.
    operation:
    - term: RNA-Seq quantification
      uri: http://edamontology.org/operation_3800
    output:
    - data:
        term: Count matrix
        uri: http://edamontology.org/data_3917
      format: []
  - cmd: ANALYSIS=1
    input:
    - data:
        term: Gene expression matrix
        uri: http://edamontology.org/data_3112
      format: []
    note: Filtering of GEF files.
    operation:
    - term: Data filtering
      uri: http://edamontology.org/operation_3695
    output:
    - data:
        term: Gene expression matrix
        uri: http://edamontology.org/data_3112
      format: []
  homepage: https://github.com/capuccino26/POLY_PIPELINE
  homepage_status: 0
  language:
  - R
  - Bash
  - Python
  lastUpdate: '2026-02-19T08:19:12.181956Z'
  license: MIT
  link:
  - note: Github Repository
    type:
    - Repository
    url: https://github.com/capuccino26/POLY_PIPELINE
  - note: Zenodo Insert
    type:
    - Other
    url: https://zenodo.org/records/18655692
  maturity: Mature
  name: Poly Pipeline
  operatingSystem:
  - Linux
  otherID:
  - type: doi
    value: doi:10.5281/zenodo.18655692
    version: v1.0.0
  owner: pedro
  publication:
  - doi: 10.5281/zenodo.18655692
    metadata: null
    note: Zenodo Insertion
    pmcid: null
    pmid: null
    type:
    - Other
    version: v1.0.0
  relation: []
  toolType:
  - Command-line tool
  - Script
  topic:
  - term: RNA-Seq
    uri: http://edamontology.org/topic_3170
  validated: 0
  version:
  - v1.0.0
- accessibility: Open access
  additionDate: '2021-04-21T22:48:24Z'
  biotoolsCURIE: biotools:open-cravat
  biotoolsID: open-cravat
  collectionID:
  - Rare Disease
  - Rare disease
  confidence_flag: tool
  cost: Free of charge
  credit:
  - email: null
    fundrefid: null
    gridid: null
    name: Kymberleigh A Pagel
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Rick Kim
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Kyle Moad
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  - email: null
    fundrefid: null
    gridid: null
    name: Rachel Karchin
    note: null
    orcidid: null
    rorid: null
    typeEntity: null
    typeRole: []
    url: null
  description: OpenCRAVAT is a new open source, scalable decision support system to
    support variant and gene prioritization. It offers a dynamic GUI, allowing users
    to easily, download tools from an extensive resource catalog, create customized
    pipelines, run jobs at speeds that exceed current variant annotation API services,
    and explore results in a richly detailed viewing environment. OpenCRAVAT is distinguished
    from similar tools by the amount and diversity of data resources and computational
    prediction methods available, which span germline, somatic, common, rare, coding
    and non-coding variants. We have designed the OpenCRAVAT resource catalog to be
    open and modular to maximize community and developer involvement, and as a result
    the catalog is being actively developed and growing larger every month.
  documentation:
  - note: null
    type:
    - General
    - API documentation
    - Installation instructions
    - Quick start guide
    - User manual
    url: https://docs.opencravat.org/en/latest/index.html
  download:
  - note: null
    type: Downloads page
    url: https://github.com/KarchinLab/open-cravat/releases/
    version: null
  - note: null
    type: Container file
    url: https://hub.docker.com/r/karchinlab/opencravat
    version: null
  editPermission:
    authors:
    - charles7
    type: group
  elixirCommunity: []
  elixirNode: []
  elixirPlatform: []
  elixir_badge: 0
  function:
  - cmd: oc run -a ANNOTATOR_LIST input.vcf
    input:
    - data:
        term: Sequence variations
        uri: http://edamontology.org/data_3498
      format:
      - term: VCF
        uri: http://edamontology.org/format_3016
    note: 'Additional input formats include: list of dbSNP rsIDs, HGVS annotation,
      and a tab-separated variant annotation format.


      Output is also in text, excel, and a SQLite database. The SQLIte database format
      can be loaded into `oc gui` as an interactive web application'
    operation:
    - term: Variant calling
      uri: http://edamontology.org/operation_3227
    - term: SNP annotation
      uri: http://edamontology.org/operation_3661
    - term: Variant effect prediction
      uri: http://edamontology.org/operation_0331
    - term: Genetic variation analysis
      uri: http://edamontology.org/operation_3197
    - term: Gene functional annotation
      uri: http://edamontology.org/operation_3672
    - term: Variant prioritisation
      uri: http://edamontology.org/operation_3226
    output:
    - data:
        term: Sequence variations
        uri: http://edamontology.org/data_3498
      format:
      - term: VCF
        uri: http://edamontology.org/format_3016
  homepage: https://opencravat.org
  homepage_status: 0
  language:
  - Python
  lastUpdate: '2026-02-18T22:04:46.355009Z'
  license: MIT
  link:
  - note: Web server for running the current version of OpenCRAVAT without needing
      a local installation.
    type:
    - Service
    url: https://run.opencravat.org/
  - note: null
    type:
    - Repository
    url: https://github.com/KarchinLab/open-cravat
  - note: Catalogue of modules for OpenCRAVAT, including annotators, variant effect
      predictors, etc.
    type:
    - Software catalogue
    url: https://run.opencravat.org/submit/nocache/index.html
  maturity: Mature
  name: open-cravat
  operatingSystem:
  - Mac
  - Linux
  - Windows
  otherID: []
  owner: rachel2
  publication:
  - doi: 10.1200/cci.19.00132
    metadata: null
    note: null
    pmcid: PMC7113103
    pmid: '32228266'
    type: []
    version: null
  relation: []
  toolType:
  - Web API
  - Web application
  - Command-line tool
  topic:
  - term: Oncology
    uri: http://edamontology.org/topic_2640
  - term: Structural variation
    uri: http://edamontology.org/topic_3175
  - term: Workflows
    uri: http://edamontology.org/topic_0769
  - term: Genomics
    uri: http://edamontology.org/topic_0622
  - term: Genotype and phenotype
    uri: http://edamontology.org/topic_0625
  - term: Rare diseases
    uri: http://edamontology.org/topic_3325
  - term: Sequence analysis
    uri: http://edamontology.org/topic_0080
  - term: Genetic variation
    uri: http://edamontology.org/topic_0199
  - term: Whole genome sequencing
    uri: http://edamontology.org/topic_3673
  - term: Exome sequencing
    uri: http://edamontology.org/topic_3676
  - term: Functional, regulatory and non-coding RNA
    uri: http://edamontology.org/topic_0659
  validated: 0
  version:
  - 2.16.0
  - 2.17.0
next: ?page=2
previous: null
