A new improved and extended version of the multicell bacterial simulator gro

摘要: gro is a cell programming language developed in Klavins Lab for simulating colony growth and cell-cell communication. It used as synthetic biology prototyping tool multicellular biocircuits. In this work, we present several extensions made to that improve the performance of simulator, make it easier use provide new functionalities. The version between one two orders magnitude faster than original version. able grow microbial colonies with up 105 cells less 20 minutes. A library, CellEngine, accelerates resolution spatial physical interactions growing dividing by implementing shoving algorithm. genetic CellPro, based on Probabilistic Timed Automata, simulates gene expression dynamics using simplified easy compute digital proteins. We also propose more convenient specification layer, ProSpec, idea proteins drive behavior. CellNutrient, another implements Monod-based nutrient uptake intercellular signaling management was improved extended library called CellSignals. Finally, bacterial conjugation, local communication process, added simulator. To show versatility potential outreach gro, studies novel examples ranging from evolutionary microbiology. believe upgrades implemented have into powerful fast capable large variety systems designs.