zhssakura
commented
5 months ago Okay. I checked the code lines in the script "Organism.R", which defined three flags that may be relevant to the lysis function: lyse, predator and feat.
The line 212 to 226 of the script described if the lyse or predator is activated, it seems the compound cpd11416 with a co-efficiency of -1 is assigned to the feat[["biomass"]] variable.
In this case, the cell "biomass" was not really broken down into its individual components, such as the carbohydrates.
This makes sense for the presence of an exchange reaction of “Ex_cpd11416_e0” in a genome-scale metabolic model, allowing it to become a predator! However, in scenarios where the network lacks a 'predator', whether lysis is on/off would not affect the metabolic interactions.
Thank you!
Dear authors,
I have some questions about the process of cell lysis in BacArena.
What happened after cells died with their lysis parameter on (lyse=T)? Would the biomass composition be released from the dead cells at the proportion of the cells' ‘minweight’? Could all biomass composition (including carbohydrates, amino acids, DNA, RNA, fatty acids and cofactors) be detected in the environment/medium? Where have those released biomass compositions been, if they cannot be reused by neighbouring microbes until the end of the simulation? Thank you for helping me!
Sincerely,
Shan