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

<p>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.</p>

<p>For visualisation in Julia specifically you could use the animation functionality of <a href="http://docs.juliaplots.org/latest/animations" rel="nofollow noreferrer">Plots.jl</a>, which is basic but there, or could try <a href="http://makie.juliaplots.org/dev/animation.html" rel="nofollow noreferrer">Makie.jl</a>. See the <a href="https://jgreener64.github.io/Molly.jl/dev/docs" rel="nofollow noreferrer">Molly.jl documentation</a> for some examples of visualising particle-type processes using Plots.jl.</p>

CC BY-SA 4.0
2020-03-19T11:07:00.953Z
2020-03-19T11:07:00.953Z
jgreener
<p>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.</p>

<p>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.</p>

<python><modelling>
Tools for modelling and visualizing growth of cells
# Tools for modelling and visualizing growth of cells

(Asked by: username_0 on 2020-03-18)

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.

**Tags:** python, modelling

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## 1 answers

### Answer by username_1 on 2020-03-19. Score: 1

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](http://docs.juliaplots.org/latest/animations), which is basic but there, or could try [Makie.jl](http://makie.juliaplots.org/dev/animation.html). See the [Molly.jl documentation](https://jgreener64.github.io/Molly.jl/dev/docs) for some examples of visualising particle-type processes using Plots.jl.


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