If you would like us to include one of your examples on this page, please send (a) the code with sufficient comments; (b) a description; (c) a link to a youtube video that shows the code running.

More examples on our youtube channel.

E. coli Nations

by Tileli Amimeur(UW), Dec. 2012

Rise of Nations meets gro! In this simulaton, strains of E. coli form nations, each with one leader to control its population. As the cells grow and divide, they get weaker/hungrier. The weaker a cell is, the darker its fluorescence. For the cells to eat and regain their strength, some must lyse (kill themselves) to release food. It is up to the leader cell ... more


by Eric Klavins(UW), Sept. 2012

In an attempt to see just how many cells gro can reasonably handle in a simulation, we let this one go for a while. The simulation shows bacterial microcolony growth, starting with five cells (although you can initially only see one). Blue represents a nutrient source. Cells emit an enzyme that breaks the nutrient down into a digestable ... more


by Andrea Samoré (University of Bologna), July 2012

A finite state machine that forms spots. Cells divide and sometimes become leader. Leaders decrease their growth rates, produce GFP and emit two different signals. The short range signal causes the closest neighbors to produce RFP while the long range one inhibits the switching to the leader state of the nearby cells.


by Eric Klavins (UW), May 2012

They run when the scent increases. They tumble, and find a new direction to go, when the scent decreases. This example demonstrates the run and tumble functions in gro (new and pretty untested in a5.2).

Coupled Oscillators

by Kevin Oishi (UW), May 2012

This example is inspired by the paper from Hasty's group on synchronized oscillators in synthetic bacteria. They used a simple network of transcription factors along with quorum sensing to achieve a self-replicating coupled oscillator. Among many innovations is their use of a microfluidic chemostat, which this ... more


by Eric Klavins (UW), April 2012

This example, which is from our recent submission on gro, produces micro-colonies with three bands of color. The initial cell divides until there are four cells. Two of them become senders of different signals. These two cells also spawn receivers. If the receivers get both signals, they grow, producing a blob of receivers between the two senders. ... more

Population Control

by Shelly Jang (UW), April 2012

In their 2004 paper, You, Cox, Weiss and Arnold showed they could use quorum sensing and programmed cell-death to regulate the density of a population. Here is demonstration of the idea using gro's chemostat mode. The cells constitutively emit a quorum sensing signal. If they sense too much of the signal, they ... more

Edge Detection

by Rehana Rodrigues, Kevin Oishi (UW), Dec. 2011

This example is derived from the one that won Rehana Rodrigues the "best simulation" award in UW's 2011 Introduction to Synthetic Biology contest. As the colony grows, cells randomly initiate waves of signaling. As the signal propogates past a particular cell, that cell can tell if it is near an edge or in the middle of the colony based on the concentration of signal ... more

For more examples see our youtube channel, or download gro!

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