Methods & Credits
Numerical verification only. This page is the license and methods notice for the local simulator. It is not a clinical validation and not a claim that the platform is an exclusively original human model.
Anatomical dataset
BodyParts3D release 4.0, 99% polygon reduction, PART-OF archive partof_BP3D_4.0_obj_99. Database Center for Life Science (DBCLS). License: Creative Commons Attribution-ShareAlike 2.1 Japan (CC BY-SA 2.1 Japan).
License statement: https://dbarchive.biosciencedbc.jp/en/bodyparts3d/lic.html. Data: https://dbarchive.biosciencedbc.jp/en/bodyparts3d/download.html.
Citation: Mitsuhashi N, Fujieda K, Tamura T, Kawamoto S, Takagi T, Okubo K. BodyParts3D: 3D structure database for anatomical concepts. Nucleic Acids Research 37, D782–D785 (2009).
The workbench applies a display rotation when the longest axis is not vertical. The OBJ files are not rewritten. Share-alike applies to adaptations of these meshes. It does not relicense the numerical engine. Mesh volume is not a simulated compartment volume. These polygons are a reference view, not a clinical segmentation.
The full local notice is assets/anatomy/NOTICE.md. Z-Anatomy was inspected and not included. A kidney mesh it cites is CC BY-NC and is not redistributed.
What a displayed number is
| Kind | Meaning in this workbench |
|---|---|
| Dynamically computed | The PBPK matrix exponential, a configured finite-volume sample, or an independent-engine scenario that was actually integrated. |
| Sampled from Pulse | Pulse 4.4.0 was advanced for that scenario. Samples are held between drug steps. The drug step does not call Pulse. |
| Prescribed | A scenario input, such as a dose or a numerical flow scale. |
| Derived | A quantity computed from another stored state, such as a concentration from amount and volume. |
| Static anatomy | A BodyParts3D mesh, or a Jones volume used as a compartment size. |
| Unsupported | Hidden unless “show unsupported fields” is on. No value is invented for it. |
External software
| Component | Role | License |
|---|---|---|
| Pulse Physiology Engine 4.4.0 | Whole-body reference runtime for scenarios that request it. Local build and PyPulse only. | Apache-2.0 |
| Three.js r160 | Vendored mesh viewer under src/hdt/workbench/static/vendor/three/. | MIT |
| NumPy, SciPy, matplotlib | Numerical arrays, ODE support, and figures. Versions in the local virtualenv. | BSD |
PK-Sim, MoBi, PhysiCell, and BioFVM are not linked. reference/ is not imported by src/hdt.
Independently developed models
The Jones and Rowland-Yeo 2013 well-mixed PBPK step, finite-volume tissue samples, the integer-microsecond scheduler, donor-limited renal exchange, closed-form gastrointestinal transit, and the independent cardiovascular and organ solvers are implemented in this repository. Standard RK4, the matrix exponential, donor limiting, and finite-volume transport are established methods. What was built here is the implementation, the accounting, and the controlled comparisons. Novelty of the underlying mathematics is not claimed.
The independent heart is an experimental backend. Its resting cardiac output stays near 3.8 L/min because the circuit was not retuned. Pulse, when the local build is present, is the portfolio physiology runtime for exercise scenarios.