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
- 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.
- 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.
- 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.
- 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.
- 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.