SkiBiDy is a hybrid agent-continuum simulation of skin tissue biology built on BioDynaMo. It models wound healing, immune response, fibroblast and collagen dynamics, scar formation, vascular perfusion, hemostasis, cellular senescence, cutaneous innervation, tumor growth, diabetic impairment, and therapeutic interventions, all from mechanistic first principles backed by DOI-linked source papers across 34 modules.
Healthy skin runs as a composite field coupling 41 diffusion grids with no agents. When an event occurs (wound, infection, tumor), cells spawn from local field state, interact with the fields, and dissolve back once stable. This is the UWYN (Use What You Need) paradigm: the simulation only creates agents where the biology demands cellular resolution.
Corneum [continuum] barrier, desquamation
Granulosum [continuum] keratohyalin, tight junctions
Spinosum [continuum] desmosomes; agents on event
Basale [continuum] stem/TA cells on event
---------- basement membrane ----------
Dermis [continuum] vasculature, O2/KGF, collagen, nerves; agents on event
source <path_to_biodynamo>/bin/thisbdm.sh
./run.sh # interactive menu
./run.sh --study=wound # punch biopsy wound healing
./run.sh --study=diabetic-wound # chronic diabetic ulcer
./run.sh --study=tumor # basal cell carcinoma growth
./run.sh --compare # normal vs diabetic side-by-side
./tests/test.sh # 130 unit tests34 modules, each self-contained in modules/ with its own config, source, data, and README. See docs/ for the full module index with biology, parameters, coupling, and validation.
| Module | Default | Module | Default |
|---|---|---|---|
| tissue | on | dermis | on |
| wound | on | elastin | off |
| immune | on | hyaluronan | off |
| inflammation | on | glucose | on |
| fibroblast | on | temperature | on |
| scar | on | lactate | on |
| mmp | on | nitric_oxide | on |
| fibronectin | on | ph | off |
| angiogenesis | on | hemostasis | off |
| perfusion | on | biofilm | off |
| diabetic | off | tumor | off |
| senescence | on | neuropathy | on |
| ros | on | bioelectric | on |
| lymphatic | on | mechanotransduction | on |
| blood | off | burn | off |
| pressure | off | scab | on |
| photon | off | body_site | off |
Config is layered TOML, merged at runtime:
bdm.core.toml core tissue params
+ modules/*/config.toml 34 module configs (auto-merged)
+ profiles/*.toml skin phenotype overlay
+ studies/*/preset.toml study experiment overlay
+ studies/*/treatments/*.toml therapeutic intervention overlay
= bdm.toml runtime config (gitignored)
Skin profiles: normal (default), aged, diabetic, aged_diabetic, rheumatoid, burn, pressure, surgical, tumor, tumor_wound. Studies: wound, diabetic-wound, tumor, tumor-wound, burn, pressure-ulcer, surgical, rheumatoid, baseline, full-model.
The diabetic treatment study compares 9 therapeutic interventions against an untreated diabetic baseline:
# Single treatment schedules (NPWT/HBO/MSC at different start days)
python3 scripts/study/gen_treatment_schedule.py --treatments npwt,hbo,msc --days 0,7,14,21
# Pairwise combinatorial scheduling
python3 scripts/study/gen_treatment_schedule.py --treatments npwt,hbo,msc --days 0,7,14,21 --combo
# Run all generated schedules
python3 studies/run_experiments.py studies/diabetic-wound/experiments/schedule_*.toml
# Full comparison study (all 9 treatments + baseline)
python3 studies/diabetic-wound/treatment.py --combos allAvailable treatments: anti-inflammatory, HBO, NPWT, doxycycline, growth factor (PDGF-BB), MSC therapy, moisture dressings, senolytic (dasatinib+quercetin), and a rational combination targeting all four dysfunction axes. See docs/treatments.md for mechanisms and references.
The RA study models synovial inflammation and cartilage erosion with a study-scoped TNF-alpha/IL-6 dual cytokine module:
# RA baseline (untreated, 10-run consensus)
python3 batch/batch.py -n 10 --skin rheumatoid --study rheumatoid
# Treatment comparison (baseline + 5 treatments)
python3 studies/rheumatoid/study.py
# Biologic comparison experiment
python3 studies/run_experiments.py studies/rheumatoid/experiments/biologic_comparison.tomlAvailable RA treatments: anti-TNF (infliximab/adalimumab), tocilizumab (anti-IL-6R), methotrexate (DMARD), JAK inhibitor, and triple combination. See studies/rheumatoid/ for details.
| Study | Profile | Treatments | Experiments | Description |
|---|---|---|---|---|
| Burn | burn |
5 (cooling, debridement, silver sulfadiazine, skin substitute, pressure garment) | 4 | Jackson's three-zone thermal injury, stasis rescue, scar prevention |
| Pressure ulcer | pressure |
5 (redistribution, wound VAC, nutrition, silver dressing, offloading) | 4 | Ischemia-reperfusion injury, stage I through IV, moisture/shear co-factors |
| Surgical | surgical |
5 (prophylactic antibiotics, chlorhexidine, negative pressure, enhanced recovery, antimicrobial suture) | 4 | SSI prevention bundles, CDC wound classes, comorbidity risk |
Shared treatments (usable across all studies) live in studies/shared/treatments/: triple antibiotic ointment.
Validated against published literature across 12 observables with per-module SOURCES.yaml files providing DOI-linked citations. Four optional mechanistic toggles (gradient-driven recruitment, efferocytosis M1 to M2, constitutive + TGF-beta collagen, HIF-1alpha VEGF) can replace parametric models for biophysical fidelity testing.
python3 batch/batch.py -n 10 --study wound --validate # parametric (default)
python3 batch/batch.py -n 10 --study full-model --validate # mechanistic toggles| Document | Description |
|---|---|
| Docs index | Module index, metrics columns, validation overview |
| Guide | Configuration, skin profiles, studies, running, visualization |
| Architecture | UWYN hybrid agent-continuum design, CompositeField, field coupling |
| Parameters | Parameter index with module links and config layering |
| Treatments | Therapeutic interventions across 6 studies |
| Studies | Packaged studies, experiments, example outputs |
| Batch | Multi-run consensus, parameter sweeps |
| Literature | Validation framework, RMSE dashboard, reference data |
| Library | Version | License |
|---|---|---|
| toml++ | 3.4.0 | MIT |
| BioDynaMo | 1.04+ (master) | Apache 2.0 (linked, not bundled) |