Virtual Cell

Learn cell biology by building a cell in code

Twelve interactive lessons that start from zero biology and end with a working simulation of a real minimal cell. Written for software engineers. The math is taught slowly, as you need it.

Start Lesson 1: The cell by the numbers

Explore

Each idea comes with something to play with: zoom from atoms to cells, guess molecule counts, drag sliders.

Understand the math

Every equation is explained one step at a time, with worked examples and "check yourself" questions.

Write the code

Python exercises run right in your browser. The functions you write become the simulator, one lesson at a time.

The cell we are building

JCVI-syn3A is a synthetic bacterium about 400 nanometers across, with only 493 genes, which makes it one of the simplest cells known that can grow and divide on its own. In 2026 researchers published a simulation of its complete life cycle in space and time (JCVI). By the end of this course you will have built your own, simpler version, and you can compare the two.

Curriculum

NoviceWhat is in a cell

  1. 1

    The cell by the numbersAvailable

    Sizes, molecule counts, and timescales, plus the math to reason about them: powers of ten, volumes, and moles.

    You build: units and constants modules

    Practice problems

  2. 2

    Molecules of lifeAvailable

    DNA, RNA, proteins, lipids, and metabolites. Water, chemical bonds, and why membranes form on their own.

    You build: sequence types and FASTA/GenBank parsing

    Practice problems

  3. 3

    The central dogmaAvailable

    How a gene becomes a protein: transcription, translation, the genetic code, and ribosomes.

    You build: transcription, translation, and a gene → protein pipeline for all 455 proteins

    Practice problems

IntermediateHow a cell runs

  1. 4

    Molecules in motionAvailable

    Diffusion, random walks, crowding, and the rates of chemical reactions.

    You build: first simulator: particles vs. ODEs

    Practice problems

  2. 5

    Enzymes and metabolismAvailable

    Enzyme kinetics, metabolic pathways, ATP as currency, and the stoichiometric matrix.

    You build: flux balance analysis

    Practice problems

  3. 6

    Gene regulation and circuitsComing soon

    Feedback, switches, and oscillators built from genes and proteins.

    You build: ODE network engine with several solvers

AdvancedMaking it realistic

  1. 7

    NoiseComing soon

    When molecule counts are small, chance matters. The Gillespie algorithm.

    You build: stochastic simulation engine

  2. 8

    Space and membranesComing soon

    Compartments, transport across membranes, and reaction-diffusion patterns.

    You build: spatial lattice model

  3. 9

    Growth, replication, divisionComing soon

    How a cell copies its DNA, divides, and decides how fast to grow.

    You build: growth and division module

ExpertWhole-cell modeling

  1. 10

    Standards and dataComing soon

    SBML, public biological databases, and fitting models to experimental data.

    You build: SBML import/export and parameter fitting

  2. 11

    Whole-cell integrationComing soon

    Combining every module into one running minimal cell, and checking it against the published syn3A model.

    You build: integrated minimal syn3A model

  3. 12

    The frontier: AI virtual cellsComing soon

    Machine-learned cell models trained on large datasets, and how they compare with mechanistic models.

    You build: optional ML surrogate for a slow module

Good books to read alongside