A New Improved and Extended Version of the Multicell Bacterial Simulator gro

gro is a cell programming language developed
in Klavins Lab for simulating colony growth and cell–cell communication.
It is used as a synthetic biology prototyping tool for simulating
multicellular biocircuits and microbial consortia. In this work, we
present several extensions made to gro that
improve the performance of the simulator, make it easier to use, and
provide new functionalities. The new version of gro is between 1 and 2 orders of magnitude faster than the original
version. It is able to grow microbial colonies with up to 105 cells in less than 10 min. A new library, CellEngine, accelerates
the resolution of spatial physical interactions between growing and
dividing cells by implementing a new shoving algorithm. A genetic
library, CellPro, based on Probabilistic Timed Automata, simulates
gene expression dynamics using simplified and easy to compute digital
proteins. We also propose a more convenient language specification
layer, ProSpec, based on the idea that proteins drive cell behavior.
CellNutrient, another library, implements Monod-based growth and nutrient
uptake functionalities. The intercellular signaling management was
improved and extended in a library called CellSignals. Finally, bacterial
conjugation, another local cell–cell communication process,
was added to the simulator. To show the versatility and potential
outreach of this version of gro, we provide
studies and novel examples ranging from synthetic biology to evolutionary
microbiology. We believe that the upgrades implemented for gro have made it into a powerful and fast prototyping
tool capable of simulating a large variety of systems and synthetic
biology designs.