HDT workbench

Mouse. Drag to orbit. Right-drag or two-finger drag to pan. Scroll to zoom. Click selects the structure under the pointer. Translucent skin is skipped unless Select skin is on or the skin opacity is high. Click the same point again to cycle overlapping structures. Double-click frames the selection. Hover highlights the target that a click would select.

Keys. F or R frames the body. 1–6 are front, back, left, right, top, bottom. Enter in the structure search frames the first match. Left and right follow the BodyParts3D lung names. Hidden meshes and the clipped side of a plane are not selectable.

Solve. Choose an experiment and press Run. Opening the page plays the stored course-correction-1 rest lattice. A stored drug run opens from Results. The playhead holds the latest stored sample. It does not interpolate. The page does not start Pulse.

Color. Organ color is one well-mixed number for the selected variable. Arteries stay red and veins stay blue. A spatial field is drawn only in the Tissue workspace, from the finite-volume sample.

Presets

Structures

Organ registry

Engineering & methods

Anatomy control

Portfolio runtime. A Pulse scenario calls Pulse 4.4.0, then the PBPK solver holds those samples on the synchronization lattice. The drug step does not advance Pulse. A static scenario uses the Jones and Rowland-Yeo flows and does not call Pulse. independent-v1, organ-v1, wholebody-v1, and course-correction-1 stay available as comparison backends. The ellipsoid body is a volume fixture.

Demonstrated and kept: donor-limited renal exchange, closed-form gastrointestinal transit, the matrix exponential for the well-stirred drug step, and mass residuals on each run. Rejected on the recorded tests: predictor-corrector exchange, step-doubling synchronization, and the 4 s / 16 s frozen-flow split (urine error 5.1 percent).

Resting cardiac output of the independent heart remains near 3.8 L/min. That backend is experimental. It is not forced into a published range.

Methods & Credits holds the license notices, citations, and the contribution inventory.

Capability matrix

Statuses describe this repository. A Pulse observation is recorded and is not an equation we integrate.

loading the capability matrix

Physiology backend

backend

independent-v1 is the default for this control. The button does not start Pulse. pulse-reference only explains that Pulse stays on its existing scenario path.

Spatial samples

A sample is a Cartesian finite-volume grid inside a parent organ. It is not the anatomical mesh.

Scenarios

rest-static is the healthy baseline. pulse-exercise compares rest, exercise, and recovery. clearance-zero removes renal clearance. Edits below are written back into the document and checked by Validate.

Left Right

Living physiology

Resting cell counts use legacy-7a. homeostasis-v1 and mean-lifespan-v1 are selected in the refinement comparison and do not replace this baseline. Pulse is not called. Counts are not drawn on the body.

No baseline is loaded.

Stored runs

Each directory is one execution. Opening it reads stored files.

Verification

The assessment reads the current models. It does not start Pulse and it does not fit them to a person. A sampled input range is not a confidence interval.

The algorithm report compares fixed-step RK4 with valve-event stepping, and the linear diastolic law with the Klotz 2006 curve. It does not start Pulse.

The comparison does not start Pulse. A thymic-output factor is not a confidence interval.

Waiting for the resting lattice.

Resting physiology

Loading the stored resting lattice.

State exchange

Pulse samples, when a scenario requests them, set organ flows. The PBPK matrix exponential then advances drug. Spatial samples, when configured, take arterial drug and return venous drug. The independent heart is a separate clock and is not the portfolio default.

Whole-body Pulse observations

No run is loaded. These readings are not painted on vessels.

Independent circulation

No independent run yet. Choose a backend and press Run selected backend.

Finite-volume sample

sample wireframe slice

Move the pointer over the field to read a cell.

Sample vessel graph

Synthetic fixture scaled to the sample perfusion. Not an anatomical artery.

Governing statement

The tissue state is an amount in moles. Concentration is amount divided by compartment volume. Diffusion is backward-Euler finite volume with no-flux faces. Vascular inlet and outlet, exchange, degradation, and metabolism are the recorded routes that change the tissue total. The mesh axes are a diffusion coordinate.

Provenance

Validate fills this table from the document. A scenario-override is an exploratory change of a literature value.

Playback

Organ function

Select an organ. The values are the stored sample at the playhead. Selection does not start Pulse.

Organ functions load with the page.

Population samples

Each sample is the exact state at that time. A schematic cell animation is not shown.

Load the resting baseline to read counts, production, and removal.

The canvas stays empty until the local sample runs. Circles are agents from that sample. The field is that sample's signal. Systemic counts are the numbers in this panel, not these marks.

Coupled run

Load a coupled scenario to read exchange fluxes at the recorded times. The display holds a stored sample. It does not interpolate.

Selected run

No run is open. Choose one from the list, or press Run.

Assessment

Load the assessment to see equations, reference checks, convergence, sensitivity, and calibration status.