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name: protocol-design description: "Routes biomedical research questions into ethically aware, feasibility-conscious study protocols covering aims, design, endpoints, bias, power, validation, and translational planning." disable-model-invocation: true metadata: disco-role: operating license: MIT

Protocol Design

Use this route when a researcher needs to turn a biomedical idea into a study-design plan: aims and hypotheses, design family, eligibility and endpoints, bias/confounding controls, sample-size logic, validation, or a translational/specialized protocol. This is protocol planning, not patient care, statistical execution, or manuscript prose.

Route and boundary

1. Frame the question. State the population/model, exposure or intervention, comparator, primary outcome, time horizon, intended estimand, and whether the claim is descriptive, associative, predictive, mechanistic, or causal-leaning. Create one coherent primary aim; subordinate secondary and exploratory aims.
2. Select the study design. Choose among experimental, clinical cohort, case-control, diagnostic/prognostic, RWE, translational, omics, or genetic (including MR) designs based on temporal logic, available data/specimens, recruitment, and the claim—not on habit. Define time-zero, eligibility, baseline window, exposure/intervention, follow-up, censoring, and endpoints.
3. Stress validity and feasibility. Separate baseline from post-baseline variables; identify selection, confounding, immortal-time, measurement, missingness, multiplicity, transportability, and competing-risk threats. Treat effect sizes, event rates, variance, follow-up, data capture, and validation resources as unknown until supported. Obtain ethics, privacy, safety, recruitment, specimen, site, and operational feasibility review.
4. Plan power and validation. Let the primary endpoint/estimand drive formal, range-based, event-driven, precision, or fixed-N feasibility planning. Specify internal versus independent, temporal/site/external, technical/orthogonal, functional, and translational validation tiers; never call resampling external validation or infer causal proof from support alone.
5. Produce a bounded handoff. Return assumptions, decisions, alternatives, feasibility blockers, minimum credible protocol, analysis/validation needs, and what remains unverified. Route live evidence retrieval and citation verification to evidence-insight, executable modeling/data checks to data-analysis, and protocol/manuscript/grant prose to academic-writing. Ethics/privacy or operational concerns may also need operations-and-audit.

Read the bundled references

• workflows.md for the end-to-end route, design families, outputs, and specialist handoffs.
• design-checklists.md for aims, eligibility, endpoints, validity, power, validation, translation, ethics, and feasibility gates.
• troubleshooting.md for missing inputs, design mismatch, unsupported assumptions, and recovery actions.

Safety and evidence limits

Do not provide patient-specific diagnosis or treatment, invent literature, registry/database capture, event rates, sample sizes, assay feasibility, validation cohorts, or ethical approval. Mark candidate resources and assumptions explicitly. A protocol draft is not an IRB/REC/IACUC submission, statistical analysis execution, or clinical decision. If a critical design input is missing, ask focused questions or proceed only with a clearly labeled provisional design and an explicit stop condition.