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

Authored by Alfonso Rodriguez-Paton, Martin Gutierrez, Paula Gregorio-Godoy, del Pulgar Guillermo Perez, Luis E Munoz, Sandra Saez

Date Published: 2017

DOI: 10.1021/acssynbio.7b00003

Sponsors: European Union Chilean National Commission for Scientific and Technological Research (CONICYT)

Platforms: C++

Model Documentation: Other Narrative

Model Code URLs: https://github.com/liaupm/GRO-LIA

Abstract

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, CelIPro, 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 CeliSignals. 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.

Tags

Individual-based model environment diffusion synthetic biology Populations Gene-expression Escherichia-coli Intercellular communication Spatial dynamics Cell-cell interactions Cell shoving algorithm Synthetic microbial consortia Multicellular biocircuits Biocad tools Gro Cell-cell communication Plasmid transfer Regulators