README.md

Home / Docs

Skin BioDynaMo (SkiBiDy) Documentation

Guides

Document	Description
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
Treatment Interventions	8 therapeutic interventions for diabetic wounds
Module Development	Step-by-step guide to adding new modules
Batch & Sweeps	Multi-run consensus, parameter sensitivity analysis
Studies	Packaged experiments, scenarios, example outputs

Module index

Each module is self-contained in modules/ with its own config.toml, source files, validation data, and README.

Core

Module	Biology	Fields
tissue	Epidermal homeostasis, cell cycle, calcium-driven differentiation	Calcium, KGF, O2, Water, Stratum

Wound healing cascade

Module	Biology	Fields
wound	Punch biopsy event, margin cell spawning	Stratum (zeros)
inflammation	Cytokine signaling, Hill-function gating	Inflammation, ImmunePressure
immune	Neutrophils, macrophages, M1/M2 polarization	(agents)
fibroblast	TGF-beta cascade, myofibroblast differentiation, collagen deposition	TGF-beta, Collagen
mmp	Matrix metalloproteinase ECM remodeling	MMP
fibronectin	Provisional matrix scaffold for migration	Fibronectin
scar	Emergent scar formation from collagen	Scar
perfusion	Vascular perfusion, angiogenesis recovery	Vascular
angiogenesis	VEGF-driven vessel sprouting	VEGF
dermis	Dermal tissue integrity, sub-layer profile	Dermis

Pathology modifiers

Module	Biology	Fields
diabetic	Chronic wound impairment across all systems	(modifier)
biofilm	Bacterial biofilm colonization, PAMP feedback	Biofilm

Neoplasia

Module	Biology	Fields
tumor	Basal cell carcinoma, soft contact inhibition	Tumor

ECM groundwork

Module	Biology	Fields
elastin	Elastic fiber network, slow turnover	Elastin
hyaluronan	Hyaluronic acid, water retention, migration scaffold	Hyaluronan

Environment

Module	Biology	Fields
ph	Wound bed pH gradient, acid mantle disruption	pH
hemostasis	Fibrin clot scaffold, platelet activation	Fibrin

Validation

The validation framework lives in literature/ with its own README. Reference data is collocated with each module under modules/<module>/data/, with citations in each module's SOURCES.yaml.

Metrics columns

The CSV written to output/skibidy/metrics.csv has 41 columns:

Column	Units	Description	Non-zero when
step	-	Simulation step	always
time_h	hours	Simulated time (step * dt)	always
time_days	days	Simulated time in days (time_h / 24)	always
n_agents	count	Active keratinocyte agents	agents spawned
n_stem	count	Stem cell agents	agents spawned
n_ta	count	Transit-amplifying agents (cycling, non-stem)	agents spawned
n_g0	count	Quiescent (G0) agents	agents spawned
n_basal	count	Agents in stratum basale	agents spawned
n_spinous	count	Agents in stratum spinosum	agents spawned
n_granular	count	Agents in stratum granulosum	agents spawned
n_cornified	count	Agents in stratum corneum	agents spawned
n_neutrophils	count	Active neutrophil agents	[skin.wound] enabled
n_macrophages	count	Active macrophage agents	[skin.wound] enabled
wound_closure_pct	%	Fraction of wound voxels with Stratum > 0.5	[skin.wound] enabled
mean_o2_wound	normalized	Mean O2 in wound cylinder	[skin.wound] enabled
mean_ca_wound	mM	Mean Ca2+ in wound cylinder	[skin.wound] enabled
mean_infl_wound	a.u.	Mean inflammation in wound cylinder	[skin.wound] enabled
scar_magnitude	a.u.	Mean scar field in wound cylinder	[skin.scar] enabled
mean_anti_infl_wound	a.u.	Mean anti-inflammatory in wound	[skin.inflammation] split_enabled
n_fibroblasts	count	Active fibroblast agents (all states)	[skin.fibroblast] enabled
n_activated_fibroblasts	count	Activated + myofibroblast fibroblasts	[skin.fibroblast] enabled
n_myofibroblasts	count	Myofibroblast-state fibroblasts	[skin.fibroblast] enabled
mean_tgfb_wound	a.u.	Mean TGF-beta in wound	[skin.fibroblast] enabled
mean_collagen_wound	a.u.	Mean collagen in wound	[skin.fibroblast] enabled
mean_perfusion_wound	normalized	Mean vascular perfusion in wound dermis	[skin.wound] enabled
n_tumor_cells	count	Active tumor cell agents	[skin.tumor] enabled
n_tumor_cycling	count	Tumor agents not in G0 (Ki-67 proxy)	[skin.tumor] enabled
tumor_field_cells	count	Tumor field voxels > 0.5 (handoff)	[skin.tumor] enabled
mean_biofilm_wound	a.u.	Mean biofilm in wound	[skin.biofilm] enabled
mean_vegf_wound	a.u.	Mean VEGF in wound	[skin.angiogenesis] enabled
mean_mmp_wound	a.u.	Mean MMP in wound	[skin.mmp] enabled
mean_fibronectin_wound	a.u.	Mean fibronectin in wound	[skin.fibronectin] enabled
mean_elastin_wound	a.u.	Mean elastin in wound	[skin.elastin] enabled
mean_hyaluronan_wound	a.u.	Mean hyaluronan in wound	[skin.hyaluronan] enabled
mean_dermis_papillary	normalized	Mean dermis integrity in papillary wound voxels	[skin.dermis] enabled
mean_dermis_reticular	normalized	Mean dermis integrity in reticular wound voxels	[skin.dermis] enabled
mean_dermis_hypodermis	normalized	Mean dermis integrity in hypodermis wound voxels	[skin.dermis] enabled
mean_ph_wound	a.u.	Mean pH alkalinity in wound	always (pH module)
mean_fibrin_wound	a.u.	Mean fibrin in wound	[skin.hemostasis] enabled
mean_ecm_quality	normalized	Composite ECM quality score	derived fields active
mean_tissue_viability	normalized	Composite tissue viability score	derived fields active

scripts/analysis/plot_metrics.py generates figures from this CSV in output/plots/.