Clinical Trial Design MCP Server

clinical-trial-design

A Claude Code plugin and MCP server for end-to-end clinical trial design.

clinical-trial-design helps biostatisticians and clinical trialists design Phase 2 and Phase 3 confirmatory studies through a conversational interface, backed by validated R statistical packages (gsDesign, gsDesign2).

v0.0.8 alpha. Pre-1.0 schema break. The ten endpoint-shaped design tools collapse into three endpoint-typed tools (design_binary, design_continuous, design_survival) with design_class ∈ {"fixed", "group-sequential"} and (for survival) model ∈ {"ph", "maxcombo", "rmst", "milestone", "wlr", "ahr"} as parameters — total tool count drops 13 → 6. Same release lifts the operational kernel into the public surface: any design tool can take an operational block that solves accrual_rate × accrual_duration = N and total_trial_duration = accrual_duration + follow_up_duration (plus a uniroot-based event-probability tie for survival). Survival accrual API standardized on accrual_duration + followup_duration for every model. 184/184 R tests pass; 14/14 smoke. Slash commands and the wire-format identifiers (designr_dispatch, DESIGNR_RSCRIPT/DESIGNR_LAUNCHER) are preserved. v0.0.6 was the rebrand from designr → clinical-trial-design; v0.0.5 was an agent-friendliness + trust-boundary release; v0.0.4 made the plugin self-contained at runtime; v0.0.3 introduced the marketplace-based install flow; v0.0.2 added Monte Carlo verification (verify_design) and markdown reporting (design_report). The current release covers fixed-sample and group-sequential designs (see MVP tool surface). Adaptive / MAMS / platform / Bayesian / recurrent-events / count-rate wrappers are roadmap, not shipped — see Roadmap. Full change history in CHANGELOG.md.

What it is

clinical-trial-design has four layers:

What clinical-trial-design actually computes

The benchmark corpus has cases across all of the above (~176 cases / 21 family directories). The current wrappers only compute the rows marked ✅. See benchmarks/README.md for the full corpus taxonomy.

Status

MVP tool surface

Nine MCP tools — three endpoint-typed design tools, three multi-hypothesis design tools, and three meta tools. Single-primary tools are organized by endpoint axis (binary / continuous / survival); multi-hypothesis tools are organized by which multiplicity pattern they encode (co-primary, multi-population, graphical). Everything else — hypothesis type, fixed vs group-sequential, survival statistical model, multiplicity strategy, accrual / follow-up timing — is a parameter.

Single-primary design tools (3)

All three accept comparison ∈ {"superiority", "non-inferiority", "equivalence"} (equivalence on binary / continuous fixed-sample only — survival wrappers don't support equivalence margins), alpha, power, sided, allocation_ratio, GS parameters (k, timing, sfu, sfl, test.type), and an optional operational block (see below).

Multi-hypothesis design tools (3) — added v0.0.8

Operational kernel

Any design tool accepts an operational block that solves the simple relations accrual_rate × accrual_duration = sample_size_total and total_trial_duration = accrual_duration + follow_up_duration (plus target_events = sample_size_total × cumulative_event_rate(...) for survival, via uniroot over the closed-form pooled exponential-PH event probability — same kernel gsDesign::nSurv uses internally).

Supply any 0–4 of {accrual_rate, accrual_duration, follow_up_duration, total_trial_duration} inside the block. The solver fills in the missing values and returns an audit trail (given, derived). This collapses what was previously a back-and-forth — call the design tool, then translate the answer into accrual feasibility — into a single round trip.

Meta tools (3)

Quick start

Prerequisites: R ≥ 4.2, Node ≥ 18. No npm install step (the MCP server ships pre-bundled in mcp-server/dist/index.js, Node deps inlined) and no remotes::install_local step (the MCP server sources r-package/ClinicalTrialDesign/R/*.R directly out of the plugin cache).

1. Clone and install CRAN dependencies (one-time)

git clone https://github.com/wei-ai-lab/clinical-trial-design
cd clinical-trial-design
R -e 'install.packages(c("gsDesign","gsDesign2","graphicalMCP","jsonlite"))'

gsDesign, gsDesign2, and jsonlite are CRAN packages the R launcher imports at runtime. Install them once into your R user library; they don't need to be reinstalled on plugin updates.

Tested dependency versions

clinical-trial-design v0.0.8 was developed and tested against the versions below. The R package's DESCRIPTION file pins minimum versions matching this set — older versions are not supported. CRAN's latest is usually fine; pin to these floors only if you hit a version-skew issue.

2. Install the plugin

Method A — slash commands (recommended, inside Claude Code)

/plugin marketplace add /full/path/to/clinical-trial-design
/plugin install clinical-trial-design@wei-ai-lab

/plugin marketplace add accepts the repo root because .claude-plugin/marketplace.json lives there. After install, restart Claude Code so it loads the bundled MCP server. Confirm with /plugin (clinical-trial-design should be listed and enabled).

Method B — host shell (equivalent, scriptable)

claude plugin marketplace add /full/path/to/clinical-trial-design
claude plugin install clinical-trial-design@wei-ai-lab
claude plugin list   # confirm: clinical-trial-design@wei-ai-lab, version 0.0.7, enabled

Both methods do the same thing. Pick one. If anything goes wrong, claude plugin validate /full/path/to/clinical-trial-design will tell you whether the marketplace + plugin manifests parse cleanly.

Quick local-dev alternative — skip the marketplace step entirely and launch Claude Code with the plugin loaded directly:

claude --plugin-dir /full/path/to/clinical-trial-design

This is for iterating on the plugin itself, not for end-user installs.

Environment overrides

If Rscript isn't on your PATH, set DESIGNR_RSCRIPT=/full/path/to/Rscript in your shell. To override the R launcher path (rare), set DESIGNR_LAUNCHER=/full/path/to/launcher.R. The MCP server reads both env vars when spawning R. (The DESIGNR_* prefix is preserved as the wire-format contract across the v0.0.6 rebrand and the v0.0.8 schema break — see CHANGELOG.)

Standalone MCP server (without Claude Code)

The MCP server is also published to npm as clinical-trial-design. Any MCP-aware client (Claude Desktop, Cursor, Continue, custom MCP host) can launch it via npx:

npx clinical-trial-design

This downloads the bundle on first run, then spawns the server on stdio. The bundle ships the staged R sources at <install>/r/inst/launcher.R — same Rscript requirement (R ≥ 4.2 + gsDesign, gsDesign2, jsonlite in your R user library), but no Claude Code plugin install needed.

Example Claude Desktop config:

{
  "mcpServers": {
    "clinical-trial-design": {
      "command": "npx",
      "args": ["-y", "clinical-trial-design"]
    }
  }
}

The plugin install path (above) is preferred for Claude Code users — it bundles the skill alongside the tools, so the agent knows how to design a trial, not just what tools exist.

Updating

When a new version is released, the update flow is:

cd /full/path/to/clinical-trial-design
git pull

…then either of these (use the same method you used to install):

Method A — slash command (inside Claude Code)

/plugin update clinical-trial-design@wei-ai-lab

Method B — host shell

claude plugin update clinical-trial-design@wei-ai-lab

Restart Claude Code afterwards so it picks up the refreshed MCP server. CRAN dependencies (gsDesign, gsDesign2, jsonlite) do not need to be reinstalled on every update — only re-run install.packages(...) if the release notes say a new dependency was added.

Uninstalling

Method A — slash commands (inside Claude Code)

/plugin uninstall clinical-trial-design@wei-ai-lab
/plugin marketplace remove wei-ai-lab

Method B — host shell

claude plugin uninstall clinical-trial-design@wei-ai-lab
claude plugin marketplace remove wei-ai-lab

Both methods are equivalent. The first command removes the installed plugin; the second removes the local marketplace pointer (skip it if you plan to reinstall later from the same checkout). Neither method touches your R library — to fully clean up, also run R -e 'remove.packages(c("gsDesign","gsDesign2"))' if you no longer need those CRAN packages for other work.

Try it

Three conversational prompts you can paste into Claude Code once the plugin is installed. Each one should invoke a specific MCP tool and return a design:

1. Fixed binary superiority (CAPTURE-style)

   "Design a trial for refractory unstable angina. Control 30-day event rate ≈ 15%, hoped-for treatment rate ≈ 9%, two-sided α = 0.05, power 80%, 1:1 allocation." Expect design_binary (design_class = "fixed") with N ≈ 1,100.

2. TTE PH group-sequential (PARADIGM-HF-style)

   "I need a 2-analysis GS design for a CV outcome trial. Control median OS ≈ 30 months, target HR = 0.75, accrual 100/month over 30 months, 24 months minimum follow-up, OBF spending, α = 0.025 one-sided, power 90%." Expect design_survival (model = "ph", design_class = "group-sequential") with events ≈ 380 at final analysis.

3. TTE NPH MaxCombo (KEYNOTE-024-style)

   "Design an immunotherapy trial with delayed effect: 4-month delay, post-delay HR 0.60, control median 10 months, accrual 20/month for 18 months, 12 months follow-up, α = 0.025, power 90%." Expect design_survival (model = "maxcombo", design_class = "fixed") with a MaxCombo design summary.

For an end-to-end example that exercises the operational kernel: append "and we can enroll 80 patients/month with at least 3 months of post-accrual follow-up — size the accrual window for me too" to prompt 1. The agent should pass an operational block containing {accrual_rate: 80, follow_up_duration: 3}, and the response will include a derived accrual duration and total trial duration alongside the headline N.

See mcp-server/SMOKE.md for the full 14-prompt smoke matrix.

Roadmap

In priority order based on the corpus's family weights:

1. Adaptive sample-size re-estimation (corpus: adaptive-ssr/) — rpact::getSampleSizeRates + custom Promising-Zone rule.
2. Group-sequential futility-only and binding-futility variants — already exposed via test.type 3–6 in current GS wrappers; add explicit anchor tests.
3. Adaptive treatment selection / population enrichment (corpus: adaptive-selection/, adaptive-enrichment/) — rpact::getDesignInverseNormal + sub-population reweighting.
4. MAMS (corpus: mams/) — rpact::getDesignMams or MAMS::mams.
5. Recurrent events (corpus: recurrent-events/) — WR::sample_size_LWYY or analogues.
6. Count / rate endpoints (corpus: count-rate/) — Poisson and negative-binomial sample size.
7. Bayesian designs (corpus: bayesian/) — wrappers around predictive-probability and posterior-probability stopping rules.
8. Platform / basket / umbrella (corpus: platform/, basket/, umbrella/) — likely separate tools per master-protocol type.
9. Simulation / OC tools (simulate_trial, compare_designs).

Each row above already has ≥ 7 curated benchmark cases ready as regression anchors.

Related work

RConsortium/pharma-skills is a complementary R Consortium working group skill collection focused on survival group-sequential designs with deep multi-hypothesis support and a Word-report deliverable backed by a Python template. As of v0.0.8, clinical-trial-design ships its own multi-hypothesis tools — design_co_primary, design_multi_population, and design_graphical_multiplicity — covering hierarchical alpha-control, biomarker subgroup + ITT patterns, and Maurer–Bretz alpha recycling. The two projects still solve adjacent problems with different shapes: clinical-trial-design is broad and MCP-native (validated tools across the gsDesign / gsDesign2 / graphicalMCP surface, no local R session needed), while pharma-skills runs in the user's local R session and requires lrsim() simulation pass before declaring a design done.

clinical-trial-design's verify_design tool adopts the same simulation-verification convention (±2 pp power / ±0.5 pp Type I tolerance) so a design produced here can be subjected to the same credibility floor.

Contributing

clinical-trial-design welcomes contributions from both human biostatisticians and AI agents. Two entry points:

• AGENTS.md — codebase tour and conventions written for AI-agent contributors (Claude, GPT, Gemini, openclaw, opencode, …). Covers the four-layer architecture, a concrete walkthrough of adding a new design wrapper, the benchmark anchor schema, and the agent-contributor protocol (one purpose per PR, paired benchmark anchor required for new wrappers, no novel methodology, no telemetry, no Co-Authored-By trailer).
• CONTRIBUTING.md — human-facing process: priority list (benchmark anchors > new wrappers > bug fixes > tool-description improvements > docs), PR checklist, and review expectations.

The highest-impact contribution is a new benchmark anchor — see .github/ISSUE_TEMPLATE/add-benchmark-case.yml for the machine-fillable template that mirrors benchmarks/schema/design.schema.json.

Trust boundary and hosting

• SECURITY.md — clinical-trial-design's statelessness as a design property: the R package and MCP server are CI-gated against disk writes and network calls (.github/workflows/security-grep.yml). Any PR introducing forbidden patterns (writeLines, saveRDS, download.file, httr::, fs.writeFile, fetch, http.request, …) fails before merge. Confidential trial inputs you give the agent never leave your conversation through the plugin.
• HOSTING.md — three deployment profiles: small-co. on public Claude Code (no persistence wanted), large-enterprise on Claude Code Enterprise + Bedrock private endpoint (corporate transcript retention as audit log), and air-gapped (forthcoming). Persistence and audit are host concerns; the plugin stays the same.

License

Apache License 2.0 — see LICENSE.