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| gro is a flexible cell programming language and powerful Agent-based Model (AbM) tool developed in Klavins Lab for simulating bacterial colony growth and cell-cell communication. It is used as a prototyping tool in synthetic biology. Here, we present some extensions made to gro to: 1) improve its performance (a new shoving algorithm and a new genetic expression module) and 2) add new functionalities (bacterial conjugation and nutrient uptake). The increase in performance is achieved mainly by the shoving algorithm that seeks to minimise calculations for relocating and reorienting simulated bacteria in the colony. The new genetic module also speeds up execution by calculating protein concentrations in each bacterium using a model based on Boolean networks with delays. | |
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