building integrative models of whole cells and their environments
AI Artwork
A collection of AI-generated illustrations that visualize ideas from our research — the principles, infrastructure, and metaphors behind computational cell biology. Each piece treats a concept as a poster: a way to think with the eye. Read top to bottom, they trace an arc — from a call to compose biology, through what a living cell is and the scales it spans, to the machine and the discipline that turn simulation into science.
I
The Call
Why compose biology at all.
We Choose to Compose
Kennedy's "We choose to go to the Moon" reimagined as a call for compositional systems biology — to look inward into the complexity of living systems and build a unified, composable science of life.
DownloadA Compositional Address
Lincoln's Gettysburg Address reimagined for the unity of biological models — that from many fragmented efforts a shared, multiscale framework shall be born, and that no model shall remain alone.
DownloadII
What a Cell Is
Lenses on the living cell — process, economy, ecology, sovereign.
The Organism as Ship of Theseus
An organism replaces nearly every molecule and cell it is made of, yet remains itself. The ancient puzzle of the ship whose planks are swapped one by one becomes biology's defining fact — identity is not the matter but the pattern that persists through continuous turnover. The cell is a process, not a substance.
DownloadThe Odyssey of the Cell
A living vessel finds its way through a sea that shapes every move. The cell as a ship — membrane hull and sail, cytoskeleton rigging, receptors on lookout, nucleus charting from memory — navigating immune storms, toxin whirlpools, siren signals, and the narrow passage of competing pressures. A cell does not command the sea from afar; it lives by navigating within it.
DownloadElements of the Cell
On boundary, self-production, and action in living form. A Euclid-style treatise on the cell — definitions, common notions, and propositions for a bounded, dissipative process that makes itself.
DownloadThe Ecology of the Cell
Ten laws of intracellular ecosystems. The cell seen as a living landscape of niches, gradients, and succession — where relation precedes identity, disturbance reveals dependency, and cells construct the very worlds they inhabit. The cell is not a machine; it is a living ecosystem.
DownloadThe Political Economy of the Cell
Ten laws of biological capital. The cell is not a machine — it is an economy that negotiates its survival under thermodynamic constraint.
DownloadThe Cell Leviathan
Eight laws of constraint. Life begins when chemistry comes under rule — boundary, surveillance, enforcement, and the sovereign that emerges from molecular obedience.
DownloadThe Machiavellian Cell
Eight rules for governance. Survival is the only objective; stability is performed, not possessed; loyalty is conditional; perception is policy; death is an instrument of statecraft. In the microscopic realm, power belongs to those who endure.
DownloadIII
Life Across Scales
The object of study, from biofilm to atom.
Multiscale Bacterial Life — Eight Scales
A continuous zoom across eight scales of bacterial life — from biofilm (~1 mm) down to atomic detail (~0.1 nm). Ecosystem, microcolony, single bacterium, cell envelope, membrane proteins, intracellular crowding, macromolecular machine, atomic structure.
DownloadMultiscale Bacterial Life — From Host to Machine
A zoom from the whole human organism through organ, tissue niche, microcolony, single bacterium, and phage attachment down to the macromolecular machine — bacterial life situated in its host tissue context across seven scales.
DownloadIV
The Machine for Discovery
The infrastructure built to model a living cell.
The Computational Vivarium
A laboratory built around a living cell simulation — scientists, robotic instruments, and AI holograms gathered around a central vivarium where a whole-cell model grows under glass. Measurement, computation, and interpretation brought into a single closed loop.
DownloadA Living Factory for Discovery
An ecosystem of models, hypotheses, and investigations around a whole-cell simulation — measurement and perturbation technologies feeding a coordinated society of AI agents that build, run, and refine models. Many ideas compete, proven ideas are expanded, and all are connected.
DownloadMultiscale Human Model Factory
Integrating measurements and models across scales — from molecules to the whole human — into one coherent atlas.
DownloadCommunity-Based Assembly of Whole-Cell Models
The ten principles of constitutional modeling. Independently-built models combine into whole-cell understanding through shared, testable interfaces and communal judgment — no model holds sovereign authority, and legitimacy comes from procedure, provenance, and use.
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How Models Earn Trust
The discipline that makes simulation science — down to its founding rules.
The Open Market of Models
Ten principles for a competitive, composable, and innovative future — where models compete, compose, and circulate as living infrastructure.
DownloadThe Model Must Graduate
No model joins the whole cell until it has earned its place. A candidate model advances through a curriculum of tests — scoped, schema-checked, and severely examined — before it is admitted into the larger whole-cell model. Membership is conferred by proof, not assertion.
DownloadThe Model Must Testify
A simulation becomes science when it can be questioned. Executable Conjecture Modeling moves evidence through a chain of custody — scoped assumptions, schema-checked artifacts, declared readouts, severe tests, three-part verdicts, and repairs that generate new predictions.
DownloadThe Model Must Pass Inspection
A model becomes credible scientific evidence only after it survives an industrial inspection line — specification, assembly, pre-run QC, stress testing, discrepancy analysis, and a decision gate — before shipping with an assurance dossier that says exactly what is claimed, how it was tested, and where it applies.
DownloadWe the Builders of Biological Knowledge
A founding charter for a unified biology, in the style of a constitution — common interfaces, FAIR data, reproducibility, and open exchange as the articles by which independently-built models compose into one science, from molecules to ecosystems.
DownloadThe Ten Commandments of Computational Cell Biology
The modeling discipline behind each component of a whole-cell model — ten rules for building biology that holds together. The foundation the whole page rests on.
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