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ACS Synth Biol. 2017 Aug 18;6(8):1496-1508. doi: 10.1021/acssynbio.7b00003. Epub 2017 May 8.

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

Author information

1
Departamento de Inteligencia Artificial, ETSIINF, Universidad Politécnica de Madrid , 28040 Madrid, Spain.
2
Escuela de Informática y Telecomunicaciones, Universidad Diego Portales , 8370190 Santiago, Chile.

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, 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.

KEYWORDS:

bioCAD tools; cell shoving algorithm; cell−cell interactions; gro; individual-based model; intercellular communication; multicellular biocircuits; synthetic biology; synthetic microbial consortia

PMID:
28438021
DOI:
10.1021/acssynbio.7b00003
[Indexed for MEDLINE]

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