A simulation that never stops
Vivarium is a garden of water, soil, weather, plants and small animals that runs day and night on a server. Its water moves by the shallow-water equations, its organisms inherit real genomes, and its animals' brains are wired from published connectomes, down to the 139,248 neurons of the fruit fly.
These figures are read from the running world every few seconds. Nothing on this page is a recording.
No animal is told where to go and no outcome is written in advance. Populations rise and fall by birth and death; behaviour is meant to come from each animal's own body, senses and nervous system. Where a written rule still stands in for a circuit, it is listed under Limits.
Wiring diagrams, constants and equations come from the scientific literature and are cited where they are used. If a number in the world cannot be traced to a measurement or a published model, it is treated as a fault to be fixed.
The simulation runs on the server and does not pause when nobody is looking. A browser only draws it. Every visitor sees the same garden, the same animals, the same weather, at the same moment.
Eight coupled systems, each on the equations and data of its own field.
The whole-brain connectome of an adult fruit fly, 139,248 neurons and 2.7 million connections, run as leaky integrate-and-fire neurons. Also the complete nervous systems of C. elegans, Platynereis and Ciona.
The shallow-water equations on a 10 cm grid over the real terrain: rain soaks in or runs off, gathers in hollows, fills them and spills. Turbulent and viscous resistance, infiltration by soil texture, evaporation from the energy balance.
At the size of an insect, water has a surface that carries, wets or traps. Which one happens follows from surface tension along the legs, the animal's weight and the force of its muscles; wet wings do not fly until they dry.
Minerals weather, litter rots, nitrogen and phosphorus cycle through microbes and roots. Ants dig their nests grain by grain in a 2.5 mm soil that slumps at its angle of repose; nothing about a nest's shape is given.
Sun and moon by orbital geometry at the garden's latitude. Light is absorbed through the air, through leaves by their pigments, and through water with the measured spectrum of H2O, which takes red thirty times faster than blue.
Growth from light, water and nutrients; stomata that open by the trade of water lost for carbon gained; a leaf energy balance; seeds, germination, competition for light. A meadow is a community, not a texture.
Every organism carries a genome. It is recombined at meiosis, mutated, and expressed as the traits of a body; species are told apart by how far their lineages have diverged. Selection is whatever lives long enough to breed.
The garden has the latitude and the climate of the wetlands of Cape May County, New Jersey: weather made by travelling fronts and lows on a simulated planet, held to the temperatures, rain and winds measured there. Not today's weather there: its climate.
A tidal creek fills and empties twice a day. The tide is computed from the constituents measured at Cape May, each driven by the sun and moon of this world's own sky, so spring tides follow its new and full moons. The water carries salt into the marsh soil; plants and animals live or die by how much they can stand.
The adult female fruit fly brain has been reconstructed neuron by neuron from electron microscopy. Vivarium runs that wiring as spiking neurons with one set of biophysical constants for every cell, the model of Shiu and colleagues, and then asks the same questions an experimenter would.
| vrest | −52 mV | vthreshold | −45 mV |
|---|---|---|---|
| τmembrane | 20 ms | τsynapse | 5 ms |
| synaptic delay | 1.8 ms | refractory | 2.2 ms |
| weight per synapse | 0.275 mV | time step | 0.1 ms |
Volunteers' computers work through the whole brain one question at a time: every sense, every one of its 8,871 kinds of cell made to fire, every kind silenced in turn, every neuron alone. Each answer is computed twice, on two different machines, and counted only when they agree.
No account. No identifier. Nothing about you or your computer is collected, and nothing is installed: a browser tab is enough.
A simulation is only as honest as its list of shortcuts. These are the present ones.
The data and models below are published science, used under the terms their authors released them under. Credit belongs to them.