rewirebio.iobenchmarks

Use cases26 questions in this release

Start from a biological question

A use case starts with a research question and your data, then explains the evidence we plan to gather, any model comparisons already collected and what they can establish for your decision. We re-check each use case against new publications every month, and each card shows when it was last checked.

Browse use cases

Browse by biological area

26 matching use cases.

  • DNA and genomes · Clinical research

    Interpret BRCA1/BRCA2 germline variants

    Evidence reviewed · 13 comparisons shown · 2 held for review · 14 tools

    Evidence check not yet recorded · re-checked monthly

    Which evidence-support methods improve BRCA1/BRCA2 variant review without increasing serious classification errors?

    You bring

    • Confirmed germline variant, reference transcript and assay limitations
    • Population frequency, segregation, phenotype and functional evidence with dates
    • A relevant, versioned ClinGen ENIGMA specification and evidence cutoff

    Opens with 13 comparisons shown · 2 held for review · 14 tools, plus limitations and sources.

    Inspect evidence and limitations →

    Related articles

    Genomic Foundation Models in 2026: What Holds Up

  • Cells and tissues · Research

    Transfer cell-type annotations to a new dataset

    Evidence reviewed · 6 comparisons shown · 4 held for review · 17 tools

    Evidence check not yet recorded · re-checked monthly

    Which annotation workflow can label my new dataset reliably and recognise unsupported cell populations?

    You bring

    • Query count data with tissue, disease, donor and assay metadata
    • A versioned reference and a defined cell-label hierarchy
    • Independent marker, protein or expert evidence where available
    • Requirements for coverage, uncertainty and resource use

    Opens with 6 comparisons shown · 4 held for review · 17 tools, plus limitations and sources.

    Inspect evidence and limitations →

    Related articles

    Genomic Foundation Models in 2026: What Holds UpView all 2 articles →

  • DNA and genomes · Clinical research

    Select a copy-number variant detection and characterisation workflow

    Evidence reviewed · 4 comparisons shown · 3 held for review · 18 tools

    Evidence check not yet recorded · re-checked monthly

    Which workflow detects and characterises copy-number changes accurately and helps an analyst assess the evidence?

    You bring

    • Whole-genome sequencing aligned reads
    • The size range and variant class (deletion, duplication, etc.) of clinical interest

    Opens with 4 comparisons shown · 3 held for review · 18 tools, plus limitations and sources.

    Inspect evidence and limitations →

  • DNA and genomes · Clinical research

    Select a DNA pathogen-identification workflow for diagnostic testing

    Evidence reviewed · 7 comparisons shown · 2 held for review · 22 tools

    Evidence check not yet recorded · re-checked monthly

    Which DNA sequencing classification workflow detects clinically relevant pathogens and handles contamination or organisms absent from the reference?

    You bring

    • Plasma microbial cell-free DNA sequencing reads
    • The reference standard available for agreement/sensitivity comparison (e.g. blood culture, composite adjudication)

    Opens with 7 comparisons shown · 2 held for review · 22 tools, plus limitations and sources.

    Inspect evidence and limitations →

  • DNA and genomes · Clinical research

    Select an execution workflow for large-scale diagnostic genomics

    Evidence reviewed · 9 comparisons shown · 8 held for review · 9 tools

    Evidence check not yet recorded · re-checked monthly

    Which eligible model configuration and execution workflow can meet a diagnostic genomics team's resource, throughput and reproducibility constraints?

    You bring

    • The diagnostic genomics team's available hardware configuration
    • The required per-sample turnaround and batch throughput

    Opens with 9 comparisons shown · 8 held for review · 9 tools, plus limitations and sources.

    Inspect evidence and limitations →

  • DNA and genomes · Clinical research

    Select an RNA pathogen-detection workflow for diagnostic testing

    Evidence reviewed · 6 comparisons shown · 28 tools

    Evidence check not yet recorded · re-checked monthly

    Which RNA sequencing workflow detects RNA pathogens reliably in the intended specimen and distinguishes real detections from host/background contamination?

    You bring

    • Respiratory specimen RNA (DNase-treated), reverse-transcribed to cDNA libraries
    • The original clinical reference assay(s) available for sensitivity comparison

    Opens with 6 comparisons shown · 28 tools · Proxy evidence only, plus limitations and sources.

    Inspect evidence and limitations →

  • DNA and genomes · Clinical research

    Review EGFR lung-cancer actionability evidence

    Evidence reviewed · 4 comparisons shown · 15 tools

    Evidence check not yet recorded · re-checked monthly

    Which systems retrieve correctly scoped sensitivity and resistance evidence for advanced EGFR-mutant NSCLC?

    You bring

    • Interpreted biomarker, genome build/transcript, histology, stage and co-alterations
    • Prior therapies, progression and sampling dates, including tissue or plasma source
    • Jurisdiction, evidence cutoff and a versioned source corpus

    Opens with 4 comparisons shown · 15 tools · Proxy evidence only, plus limitations and sources.

    Inspect evidence and limitations →

  • Cells and tissues · Research

    Assess models for genetic perturbation experiments

    Evidence reviewed · 6 comparisons shown · 8 held for review · 29 tools

    Evidence check not yet recorded · re-checked monthly

    Which prediction methods and controls should I test before using expression predictions to plan genetic perturbation experiments?

    You bring

    • Single-cell expression measurements from perturbed and unperturbed cells, with perturbation and cell-type labels
    • A study design with multiple measured perturbations and cells per perturbation; combinations require combination examples during GEARS training

    Opens with 6 comparisons shown · 8 held for review · 29 tools, plus limitations and sources.

    Inspect evidence and limitations →

    Related articles

    Genomic Foundation Models in 2026: What Holds UpView all 2 articles →

  • Metabolomics · Research

    Shortlist molecular identities from tandem mass spectra

    Evidence reviewed · 7 comparisons shown · 9 tools

    Evidence check not yet recorded · re-checked monthly

    Which retrieval configurations merit validation when molecular formula is unknown and a researcher can examine only a short list of candidate structures?

    You bring

    • MS/MS spectra with metadata sufficient to derive neutral molecular mass
    • A frozen set of candidate molecular structures; the true identity must be present for the measured retrieval endpoint

    Opens with 7 comparisons shown · 9 tools · Proxy evidence only, plus limitations and sources.

    Inspect evidence and limitations →

  • DNA and genomes · Clinical research

    Select a patient-RNA splicing-variant validation workflow

    Evidence reviewed · 7 comparisons shown · 1 held for review · 23 tools

    Evidence check not yet recorded · re-checked monthly

    Which DNA/RNA evidence workflow identifies splice-altering variants for inherited-disorder follow-up when patient RNA and tissue-specific context are available?

    You bring

    • Patient skin-fibroblast (or matched tissue) RNA-seq aligned reads
    • The number of samples available for a FRASER-style aberrant-splicing cohort

    Opens with 7 comparisons shown · 1 held for review · 23 tools, plus limitations and sources.

    Inspect evidence and limitations →

What a use case shows

  1. Question and inputsThe biological question, who it is for and the data you would start with.
  2. Relevant evaluationsBenchmark protocols whose endpoint matches the question directly or only as a proxy.
  3. Tested models and resultsThe exact model configurations and controls evaluated, with the recorded scores and their sources.
  4. Limits and missing evidenceWhat does not transfer to your setting, what has not been measured and how the page was reviewed.

Use cases, benchmarks or models?

Use cases (this page)
You have a research question and data, and want to know which evaluations and models are relevant.
Benchmarks
You want one benchmark's tasks, protocols, datasets and published results.
Models
You already know a model and want its evaluations, configurations and how to run it.

Research relevance and clinical evidence

Each question states its setting, endpoint and transfer limitations. A relevant assay result does not by itself establish clinical performance. Clinical research pages explain which patient or workflow questions the available evidence leaves unanswered.

About this collection

User questions lead evidence gathering. A question can enter this collection before model comparisons have been collected: its plan states what to compare, how to validate it and what to collect next.

Where reviewed evidence is available, inspect the exact configurations, evaluation protocols and source-linked results. Incompatible protocols remain separate. Review method, research or clinical research scope, and missing evidence stay visible.

Contribute evidence or a correction · Evidence and review methods

Release and downloads

Release 2026-10-12-fcce59cc481b

Use-case input digest 35f52add6b109da224409bbf706eb584e4b963c80a0c952cc0448d88fc9b3bfc

Download questions, collection plans and applicability mappings (JSON) (gzip)

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