Reference¶

Parameter values, MCP tools, prompt files, and the file map. Everything you would want to look up quickly without re-reading the narrative pages.

Parameter reference¶

All parameters live in model/cardiac_params.m.

Variable	Default	Units	Used in	Notes
`beta_blocker_dose_mg`	50	mg	`BetaBlockerDose` Constant	The dose the demo changes in Prompt 3.
`pk_time_constant`	1800	s	`BetaBlockerPK / PKTransferFcn` denominator	30 min effective time constant.
`baseline_heart_rate`	75	bpm	`HeartRateModel / BaselineHR`	Drug-free resting HR.
`emax_bpm`	18	bpm	`HeartRateModel / HillEquation` Fcn	Maximum drug-induced HR reduction.
`ec50_mg`	35	mg	`HeartRateModel / HillEquation` Fcn	Concentration for half-maximal effect.
`hill_n`	1.5	—	`HeartRateModel / HillEquation` Fcn	Hill coefficient (binding cooperativity).
`stroke_volume_mL`	70	mL/beat	`CardiacOutputModel / StrokeVolume`	Constant in this demo.
`svr_mmHg_min_per_L`	18	mmHg·min/L	`BloodPressureModel / SVRGain`	Constant in this demo.
`map_setpoint_mmHg`	94	mmHg	`BaroreflexController` set-point	Target MAP the baroreflex defends.
`baroreflex_gain`	0.30	bpm/mmHg	`BaroreflexController` Gain	Feedback gain from MAP error to HR.
`baroreflex_tau`	60	s	`BaroreflexController` lag	First-order lag on the reflex.

Derived constants (printed at startup, not used by Simulink):

Quantity	Description	Value at default dose
`expected_HR_baseline_bpm`	Closed-loop steady-state HR	67.4 bpm
`expected_CO_baseline_Lmin`	\(\text{HR}_{ss} \cdot \text{SV} / 1000\)	4.72 L/min
`expected_MAP_baseline_mmHg`	\(\text{CO}_{ss} \cdot \text{SVR}\)	84.9 mmHg

Model configuration¶

Setting	Value	Set in
Solver	`ode45`	`create_cardiac_model.m`
Solver type	Variable-step	`create_cardiac_model.m`
`StopTime`	`3600` (s) by default; overridden to `9000` in full-validation runs	`create_cardiac_model.m`
`MaxStep`	`10` (s)	`create_cardiac_model.m`
`EnablePacing`	`off` by default; `on` during the dashboard	toggled by `realtime_dashboard.m`
`PaceRate`	`0.005` (wall sec per sim sec) when pacing is on	`realtime_dashboard.m`

MCP tools used by the demo¶

The matlab-simulink MCP server (defined in .github/mcp.json for Copilot CLI and in .vscode/mcp.json for VS Code) exposes both Simulink graph tools and MATLAB code tools. Every prompt in the demo routes to one or more.

Simulink tools¶

Tool	Used in	Purpose
`model_overview`	Prompt 1	Subsystem hierarchy and interface summary.
`model_read`	Prompts 1, 2	Block topology, connections, computed expressions.
`model_query_params`	Prompt 2	Random access to block parameters not in `model_read`.
`model_resolve_params`	Prompts 2, 3	Resolve workspace variables to numeric values.
`model_edit`	Prompt 3 (parameter form)	Structural and parameter changes to the model.
`model_test`	Prompt 6	Gherkin-driven Simulink Test harness creation and run.
`model_check`	(optional)	Lint for unconnected ports, dangling lines, Stateflow issues.

MATLAB tools¶

Tool	Used in	Purpose
`evaluate_matlab_code`	Prompts 3, 4, 7	Direct MATLAB execution in the shared session (`assignin`, `sim`, `slreq.*`).
`run_matlab_file`	Setup, demo, dashboard	Execute a `.m` script end-to-end.
`run_matlab_test_file`	(optional)	Run a `matlab.unittest.TestCase` via `runtests`.
`check_matlab_code`	Pre-commit	Static analysis on a `.m` file.
`detect_matlab_toolboxes`	Diagnostics	List installed toolboxes when a feature requires one.

The tools are loaded automatically when Copilot is invoked — in VS Code Agent mode via the workspace-level .vscode/mcp.json, or from the copilot CLI via the repo-level .github/mcp.json.

Prompt files¶

Each prompt is a reusable Copilot slash command, stored in .github/prompts/.

File	Slash command	Demo step
`01-explore-model.prompt.md`	`/01-explore-model`	Prompt 1. Architecture overview
`02-find-dosage-parameter.prompt.md`	`/02-find-dosage-parameter`	Prompt 2. Locate dose parameter
`03-apply-dose-change.prompt.md`	`/03-apply-dose-change`	Prompt 3. Apply +20 % change
`04-run-simulation.prompt.md`	`/04-run-simulation`	Prompt 4. Run and compare
`05-interpret-clinical-impact.prompt.md`	`/05-interpret-clinical-impact`	Prompt 5. Clinical interpretation
`06-generate-validation-test.prompt.md`	`/06-generate-validation-test`	Prompt 6. Gherkin test
`07-generate-requirements.prompt.md`	`/07-generate-requirements`	Prompt 7. Engineering requirements
`08-realtime-dashboard.prompt.md`	`/08-realtime-dashboard`	Prompt 8. Real-time dashboard

File map¶

Path	What it is
`model/cardiac_params.m`	Workspace parameters.
`model/create_cardiac_model.m`	Builds `CardiacDigitalTwin.slx`.
`model/run_simulation.m`	Headless run and comparison plot.
`validation/beta_blocker_dose_response.feature`	Gherkin verification test.
`validation/validate_beta_blocker.m`	MATLAB validation suite.
`validation/validation_criteria.md`	10 pass/fail acceptance criteria.
`demo/live_prompts.md`	The 8-prompt narrative.
`demo/scripted_runbook.md`	Pre-verified fallback outputs.
`demo/narrative_script.md`	Executive narration.
`demo/realtime_dashboard.m`	Live `uifigure` dashboard.
`CardiacDigitalTwin_Requirements.slreqx`	Engineering requirements artifact.
`setup/startup.m`	MATLAB session initialiser.
`setup/mcp-configuration.md`	MCP setup guide.
`setup/preflight_checklist.md`	Pre-demo verification.

What is and is not committed¶

Pattern	Status	Why
`model/.m`, `validation/.m`, `demo/*.m`	tracked	Source of truth (scripts, not binaries).
`*.feature`	tracked	Gherkin tests are hand-authored.
`*.slreqx`	tracked	Engineering requirements are hand-authored.
`.md`, `mkdocs.yml`, `docs/*`	tracked	Documentation.
`.github/**`, `.vscode/mcp.json`	tracked	Repo-level Copilot and MCP configuration (`.github/mcp.json` for Copilot CLI, `.vscode/mcp.json` for VS Code).
`CardiacDigitalTwin.slx`	gitignored	Built by `create_cardiac_model.m`.
`.slxc`, `slprj/`, `.mat`	gitignored	Build and cache artifacts. Regenerated on every build.
`.autosave`, `~mdl.slmx`, `*_harnessInfo.xml`	gitignored	Transient Simulink editor and test files.

The result: the entire model and every engineering artifact are reproducible from a clean clone. Run startup.m, and the .slx, the harness, the slprj/ cache, and any required parameter state are all regenerated locally.

Building this documentation site¶

pip install -r docs-requirements.txt
mkdocs serve          # local preview at http://127.0.0.1:8000
mkdocs build          # produce a static site in ./site/

The site uses Material for MkDocs, Mermaid for diagrams, and MathJax for formulas. All configuration is in mkdocs.yml.

Versions tested¶

Component	Version
MATLAB	R2025a, R2026a
Simulink	bundled with the MATLAB versions above
Simulink Test	required for Gherkin verification
Simulink Requirements Toolbox	required for the `.slreqx` artifact
Simulink Agentic Toolkit	latest release
GitHub Copilot	Agent mode + MCP enabled
VS Code	latest stable (or Insiders)
MkDocs Material	9.5 or newer