I am looking for a program/GUI app/package that would help me do simulations for cell growth. I have a microscopic mathematical model, and the scenario is basically the following: I start with a rod-shaped cell characterized my its center and direction angle, it grows until it reaches a certain length, it divides into two identical cells whose angles change randomly and the process continues.

Is there any program or package that I can use for such a situation? I have found several on GitHub, but they were mostly for very complicated biological processes. I use Python/Julia/Matlab and can code, but I was wondering whether there are any tools for such simpler scenarios.


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If the scenario is simpler, and you can't find anything by searching, I would consider just writing your own.

The modelling can be done in any language but if compute time is an issue - for example you want to run a simulation with many cells or many simulations - then I would use a language that can support that such as Julia or NumPy in Python. In fact Julia is a nice language for this type of thing as you end up with readable code that runs fast.

For visualisation in Julia specifically you could use the animation functionality of Plots.jl, which is basic but there, or could try Makie.jl. See the Molly.jl documentation for some examples of visualising particle-type processes using Plots.jl.


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