Move through 3D space
Rotate the cell, pan, zoom and inspect structures from different viewpoints. Support mouse, touch and keyboard first, then VR controls.
A separate product roadmap · Updated 1 October 2026
4D Virtual Cell, built one layer at a time.
Start with the published Chapter 1 prototype. Add molecular detail, then show how those parts work together. Each module should be useful on its own and connect to the model before it.
How to use the book: Essential Cell Biology, 6th edition, provides a sequence of topics—not text, diagrams, or a specification to copy. Build original explanations and visuals, verify them against primary sources, and add a chapter module only when its science and interactions have been reviewed.
4D: explore space and time
Build an interactive cell in three-dimensional space, with time as the fourth dimension. Molecular movement must connect to the function being explained.
Control time
Play, pause, replay, seek and adjust speed. Show the process time scale and preserve the selected moment while exploring the cell.
Watch molecules work
Connect motion to diffusion, transport, binding, catalysis and molecular motors. Show representative molecules and expand coverage through reviewed modules.
Test biological fidelity
Separate illustrative trajectories from measured or validated dynamics. Identify assumptions, spatial scale and time scale for each process.
Next foundation: one human cell type, a navigable 3D model and one time-controlled molecular process. Expand differentiated cell types and mechanical detail after review.
Long-term direction: an inspectable virtual-cell simulator
AIDO Cell is a useful reference for the ambition: its article describes a cell state that carries across experiments, accepts interventions, and returns different readouts from the same state. It also describes a research system built and benchmarked for selected cell lines—not a general-purpose product we can reproduce by adding more animation.
Read GenBio AI’s AIDO Cell overview
Near term · make the model inspectable
Keep building the learning model and chapter modules. Label what is illustrated, measured, inferred, or unknown.
First simulator slice · one bounded experiment
After choosing a cell context and a well-supported pathway, let a user change one intervention, reset or branch the starting state, and compare a few linked outputs. Show the rules and sources behind every change.
Expand only with evidence
Add more pathways, time steps, or readouts when reliable data supports them. Keep outputs from one experiment internally consistent and expose uncertainty.
Research-grade system · a later goal
Only pursue data-trained, multi-scale predictions after assembling suitable experimental datasets, independent benchmarks, scientific partners, and a validation plan.
Recommended first milestone: a small, transparent perturbation sandbox for one cell context and one pathway—not an AI model that claims to predict whole-cell behavior. No such predictive simulator is built or validated in the current prototype.
Build sequence
The order follows the book’s 20 chapters. Chapters are grouped where a shared model or dependency makes implementation more coherent.
1 · Establish the cell
Chapter 1 is the current published foundation.
Chapter 1
Cells: The Fundamental Units of Life
Compare animal, plant, and bacterial cells; explore scale, microscopy, diversity, and a simple information path.
Current prototype · expand after learner review2 · Add the molecular toolkit
Next: build the smallest pieces needed to explain cellular mechanisms.
Chapter 2
Chemical Components of Cells
Introduce water, ions, small molecules, and the major classes of biological molecules with a scale-aware molecular inventory.
Chapter 3
Energy, Catalysis, and Biosynthesis
Show how enzymes and energy-carrying molecules support reactions; let learners trace inputs, transformations, and outputs.
Chapter 4
Protein Structure and Function
Explore a protein’s shape, binding partners, and activity; connect a molecule’s structure to its job.
3 · Make information visible
Connect genome organization to expression, regulation, and evidence.
Chapter 5
DNA and Chromosomes
Show DNA packaging and chromosome organization at linked scales.
Chapter 6
DNA Replication and Repair
Build a stepwise replication and repair view, with errors and repair outcomes clearly distinguished.
Chapter 7
From DNA to Protein: How Cells Read the Genome
Expand the current DNA → RNA → protein sketch into transcription, RNA processing, and translation.
Chapter 8
Control of Gene Expression
Let learners compare how cells use different parts of the same genome.
Chapter 9
How Genes and Genomes Evolve
Compare conserved and changed features across organisms without implying every model result transfers to humans.
Chapter 10
Analyzing the Structure and Function of Genes
Connect questions to methods and evidence: what each technique can show, and what it cannot.
4 · Build the cell’s working environment
Put membranes, transport, energy, compartments, and signaling into one navigable system.
Chapter 11
Membrane Structure
Explore the membrane as a selective, dynamic boundary with embedded proteins.
Chapter 12
Transport Across Cell Membranes
Compare passive movement, channels, carriers, and pumps with controllable concentration gradients.
Chapter 13
How Cells Obtain Energy from Food
Trace food breakdown and energy transfer through a simplified, linked pathway.
Chapter 14
Energy Generation in Mitochondria and Chloroplasts
Zoom into energy conversion while distinguishing mitochondria from photosynthetic chloroplasts.
Chapter 15
Intracellular Compartments and Protein Transport
Follow protein destinations and vesicle traffic across cell compartments.
Chapter 16
Cell Signaling
Let a signal move from receptor to intracellular response, with branching and feedback shown carefully.
5 · Show movement, inheritance, and communities
Finish the chapter sequence by connecting cell behavior to tissues and organisms.
Chapter 17
Cytoskeleton
Make cell shape, internal tracks, movement, and force understandable through manipulable filaments and motors.
Chapter 18
The Cell Cycle
Explore cycle stages, checkpoints, and cell division as a controlled sequence.
Chapter 19
Sexual Reproduction and Genetics
Connect chromosome inheritance, genetic variation, and probability to cell-level events.
Chapter 20
Cell Communities: Tissues, Stem Cells, and Cancer
Link cell specialization, tissue organization, renewal, and cancer-relevant changes without reducing disease to one cause.
Build each module in this order
Write the learning goal
One question, one audience, and a short explanation of what a learner should understand.
Map the science
Use primary research and trusted references; mark uncertainty, context, and model limits.
Design the interaction
Choose a useful comparison, zoom, sequence, or control—not interaction for its own sake.
Create original visuals
Use clear labels, scale cues, and consistent visual language. Never present a schematic as a micrograph.
Review and test
Check content with subject experts and test comprehension, accessibility, and small screens.
Connect and release
Link the module to earlier concepts, publish only after review, and record sources and limitations.
Release gates
Scientific accuracy
Every claim has a traceable source and a clear boundary between established evidence and simplification.
Learning value
A learner can explain the idea more clearly after using the model; measure this before adding more detail.
Honest visuals
Label schematic, scale, and uncertainty. Show zoomed organs or molecular structures only when the cue is reviewed.
Accessible interaction
Keyboard, touch, reduced-motion, readable labels, and a useful non-animation explanation all work.
Toward a model useful for drug development
The viewer currently supports inspection and hypothesis communication. It does not predict efficacy, toxicity, target engagement or dose response.
Reference scale — implemented
30 µm cell diameter and 5 µm nucleus reference; mitochondria use 1.5–2 µm length and 0.6 µm width assumptions. Ribosomes use 25 nm diameter; microtubules use 25 nm width and actin uses 7 nm width. These are representative dimensions, not universal values. ER and Golgi geometry remain schematic.
Select and follow — implemented
Search a catalog of 20 modeled components, choose a representative instance, focus or follow it, and seek through an illustrative 20-second sequence. Tiny visibility markers are enlarged independently of the reference geometry. Drug-sized probes have no drug-specific chemistry.
Measured human cell geometry — next
Import microscopy-derived organelle surfaces with cell type, culture conditions, segmentation confidence, imaging scale and licensing. Begin with one well-characterized human cell dataset; add differentiated types separately.
Molecular identity and localization
Connect curated protein identifiers, isoforms, structures, copy numbers, concentrations and compartment localization. Add nuclear-envelope continuity, membrane thickness, organelle subcompartments and contact sites from reviewed data.
Mechanisms and dynamics
Replace illustrative paths with models of diffusion, crowding, binding, transport and reactions. State units, kinetic parameters, boundary conditions, uncertainty and calibration data. Add membrane trafficking, mitochondrial remodeling and cytoskeletal forces in bounded modules.
Drug-specific evidence
Add a named compound only with sources for structure, physicochemical properties, permeability, target binding and relevant cellular exposure. Track target occupancy, pathway response and assay endpoints only after validation against independent experimental data.
Scalable detail
Use multiscale views, instanced rendering, spatial indexing and compartment-based loading. A searchable biological catalog should distinguish known entities from rendered representative instances; no screen can individually display every molecule at once.
Validation and reproducibility
Record dataset versions, random seeds, model assumptions and parameter provenance. Compare morphology and localization against imaging, dynamics against tracking experiments, and predicted responses against held-out assays. Subject experts must review each supported use.
Sources: NIGMS · organelle dimensions; Molecular Biology of the Cell · mitochondrial form and motion; Allen Integrated Cell · measured human-cell organization; Allen Cell · imaging resources.
Research-informed refinements
Cell organization depends on context
Viana and colleagues studied human induced pluripotent stem cells and quantified structure organization across cell shapes and states. Our generic reference geometry is not a reconstruction from their dataset. The next data-backed step is a specific cell population with distributions of morphology and localization.
Viana et al. · Nature, 2023Contact sites connect distinct membranes
Obara and colleagues combined imaging and molecular tracking to study ER–mitochondria interfaces and VAPB dynamics. The viewer now includes a selectable contact illustration with separate membranes. Its gap and location are assumptions; it does not reproduce their measurements or transfer kinetics.
Obara et al. · Nature, 2024Geometry and behavior are separate evidence layers
The expanded ER network and nuclear envelope are explanatory geometry. Follow views now center on structure bounds, including elongated networks. Activity stops at its endpoint. Importing experimental trajectories, uncertainty and cell-state metadata remains necessary before using this model to evaluate a compound.
Reading guide
This roadmap follows the 20 chapter titles in the sixth edition. The chapter names are used as an outline; all explanations and visuals on this site are original.
Publisher · Essential Cell Biology, 6ePublisher · chapter listPublisher · Chapter 1This is a proposed build sequence, not a delivery-date promise. Later phases depend on learner testing, scientific review, available time, and the quality bar of earlier modules.