Virtual Cell SBS MC Workstation | Project Adam x KPT

Schematic - not microscopy

Select a structure to inspect its mechanism and implementation boundary. Geometry is schematic; organelle size and placement are not measured.

Time series

State proxies (a.u.) / model-hours. ATP: teal; lactate: navy; ROS: orange.

Genome-scale metabolism

Browse

Steady-state flux analysis

Retained baseline uses the upstream model's default bounds and biomass objective. Its permissive medium is not a measured hiPSC growth condition. Units: mmol/gDW/hour.

Standalone HTML browses the full network and retained result. New FBA solves require the included Python service. Dynamic supply controls do not modify FBA bounds.

Mechanism inventory

Book doctrine -> source registry -> typed ports -> local solver -> witness -> Project Adam boundary.

Inventory coverage measures these 18 declared modules only. It does not measure a percentage of human biology.

ID / mechanism	Executable scope	State / gap

Project Adam admission

The included adapter validates a supplied BiologicalStatePatch and its hash, then emits a schema-conforming PARTIAL CellAgentStatePacket. No upstream patch is invented. Tissue and organ admission remain blocked pending evidence and coupling contracts.

python adam_adapter.py --patch SOURCE_PATCH.json --dynamics DYNAMICS_RECEIPT.json --output CELL_PACKET.json

Ports

Project Adam x KPT

KPT's actual 118-element identity registry is mounted here. A local bridge maps explicit molecular formulas to element IDs and audits reaction stoichiometry and charge.

BOUNDARY: single-species exchange, sink or demand. UNCHECKABLE: unresolved formula or charge. IMBALANCED includes aggregate and pseudo reactions; review context before treating it as a model defect. These are local audit categories, not canonical KPT VM gate results.

Reaction	Element residual	Charge residual	Missing species data

The first 100 matching records appear below. The complete audit is available through export.

KPT identity registry

Authority boundary

The workstation does not add programs to the canonical KPT admitted-program list, modify KPT gate state, or treat an identity match as a kinetic or empirical witness.

Evidence and validation

Book: Kevin Flint, Foundations of Synthetic Biology: Bridging Biology with Advanced Mathematical Frameworks, 100 pages. Multiscale framework: pp. 16-22; biological networks: chapter 3; ODE, stochastic and agent models: pp. 52-60; code hooks: pp. 97-100.
Reference context: human induced pluripotent stem cell. Allen's resources ground structural scope; no Allen image or cell-specific measurement was imported. Allen Integrated Cell / data resources.
Human-GEM: version 2.1.1. Actual SBML model is pinned and included with upstream CC BY 4.0 license. Upstream model.
Project Adam: actual cell/patch schemas and hashing implementation retained. Adapter is additive; source patch lineage beyond shape and hash is not verified.
KPT: actual element registry retained. Local formula audit does not inherit scientific gate state.
VMF hooks: modular state-vector evolution and nonlinear/linear couplings are implemented locally. SGFE, SDF, ITO, QCAGR and IMA are mapped as doctrine; calibrated quantum or universal cross-scale solver execution is not asserted.

Validation receipt

Open build requirements

Reproduction

python -m pip install -r requirements.txt
python build_network.py
python kpt_bridge.py
python -m unittest -v test_workstation.py
node test_dynamics.js
python package_workstation.py
python serve.py
# Open http://127.0.0.1:8765

Full authored code

Every authored source file is available here. The source bundle also contains the full upstream SBML, license, provenance, schemas, tests and retained receipts.

Source file