Remove a cell from the simulation

[alexweisberg]

Thank you for your patience with these questions. I am wondering if it is currently possible to remove a cell completely from a simulation? Essentially to simulate a cell "lysing" or otherwise being removed from an environment? Currently it is easy to set the growth rate to zero and change the cell type to treat a cell as "dead" however it still takes up space in the simulation as debris. Simulator.py has addCell() but there is no equivalent removeCell() or similar that I could find.

[danieljones333]

Just wondering if anyone has found a good way to do this? This would be very useful for simulating e.g. cell populations growing in microfluidic devices where cells are flushed away as they grow outside of a defined area.

[timrudge]

Hi - I have created a branch with a working version of cell death (ie. remove a cell from sim) here. There is now a flag that can be set on each cell called killFlag. Set it to True to remove the cell. This requires some more testing and conversion of integrators (currently on CLEulerIntegrator is working). I will keep working on it slowly...

[gugagog]

Hello,

I really appreciate your help with installing the software. I was curious if you got a chance to add killFlag init CLCrankNicIntegrator.

Thank you!

[timrudge]

The death branch needs some work to get all the modules working, any help here would be appreciated. The principle is to keep a list of indices of live cells and update this when cells die or are created.

[ar-valdez]

@timrudge Is there a way to "swap" the cell with killFlag to the end of the cell array, and later remove the last cell?I'll try that and let you know my success... (or failure)