rewire.itbenchmarks

Use cases17 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.

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.

Browse use cases

Browse by biological area

17 matching use cases.

  • DNA and genomes · Clinical research

    Interpret BRCA1/BRCA2 germline variants

    Collection planned

    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 0 evaluated endpoints · 0 tested configurations · No current evaluated evidence, plus limitations and sources.

    View question and evidence plan →
  • Cells and tissues · Research

    Transfer cell-type annotations to a new dataset

    Collection planned

    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 0 evaluated endpoints · 0 tested configurations · No current evaluated evidence, plus limitations and sources.

    View question and evidence plan →
  • DNA and genomes · Clinical research

    Review EGFR lung-cancer actionability evidence

    Collection planned

    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 0 evaluated endpoints · 0 tested configurations · No current evaluated evidence, plus limitations and sources.

    View question and evidence plan →
  • Cells and tissues · Research

    Assess models for genetic perturbation experiments

    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 2 evaluated endpoints · 4 tested configurations · Proxy evidence only, plus limitations and sources.

    Inspect evidence and limitations →
  • Metabolomics · Research

    Shortlist molecular identities from tandem mass spectra

    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 4 evaluated endpoints · 6 tested configurations · Proxy evidence only, plus limitations and sources.

    Inspect evidence and limitations →
  • Cells and tissues · Research

    Select perturbations for a defined cellular response

    Collection planned

    Which genetic perturbations should I test to produce a defined cellular response?

    You bring

    • A defined cell system, starting state and target phenotype
    • Candidate genetic perturbations and a fixed testing budget
    • Measured perturbations and matched controls with guide, replicate and condition metadata
    • The intended transfer setting: unseen genes, combinations or a new cellular context

    Opens with 0 evaluated endpoints · 0 tested configurations · No current evaluated evidence, plus limitations and sources.

    View question and evidence plan →
  • DNA and genomes · Research

    Compare methods for plant promoter experiments

    What evidence supports choosing a sequence model for predicting plant core-promoter strength in the intended reporter assay?

    You bring

    • A 170 bp core-promoter sequence spanning −165 to +5 relative to an annotated transcription start site
    • The sequence species and intended assay host: maize protoplasts or tobacco leaves

    Opens with 6 evaluated endpoints · 4 tested configurations · Proxy evidence only, plus limitations and sources.

    Inspect evidence and limitations →
  • Proteins and complexes · Research and Clinical research

    Assess methods for protein stability experiments

    What evidence supports ranking protein substitutions by folding stability, and what must be validated before choosing a method?

    You bring

    • Wild-type protein sequence and amino acid substitutions
    • A defined construct and experimental stability endpoint; alignment-derived methods additionally require a traceable alignment and model

    Opens with 2 evaluated endpoints · 2 tested configurations · Proxy evidence only, plus limitations and sources.

    Inspect evidence and limitations →
  • DNA and genomes · Clinical research

    Rank rare-disease variants for review

    Collection planned

    Which methods recover causal variants and genes within a realistic laboratory review budget?

    You bring

    • Quality-controlled variant calls, genome build and calling coverage
    • Phenotype terms, pedigree, inheritance and available family sequencing
    • Dated population-frequency and gene–disease evidence

    Opens with 0 evaluated endpoints · 0 tested configurations · No current evaluated evidence, plus limitations and sources.

    View question and evidence plan →
  • DNA and genomes · Research

    Select regulatory variants and genes for functional follow-up

    Collection planned

    Which variants, regulatory elements and genes should I perturb to explain a disease-associated locus?

    You bring

    • Fine-mapped variants with genome build, ancestry and linkage-disequilibrium context
    • Candidate regulatory elements, genes and a relevant cell type
    • Sequence and available chromatin, expression or contact measurements
    • The feasible perturbation assay, readout and follow-up budget

    Opens with 0 evaluated endpoints · 0 tested configurations · No current evaluated evidence, plus limitations and sources.

    View question and evidence plan →

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 2026-09-29-06401fd5b220

Use-case input digest a0dd27a5f430ec387d309fd6e8615083250873ce4cff5e882c6fb8458ef80e95

Download questions, collection plans and applicability mappings (JSON)

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