I’m using Julia to program multicellular simulations.
It’s working well and the simulations are very fast, but basically I was never able to use other packages in the core of my simulations.
I read this preprint:
which contains this plot of software frameworks for multicellular simulations
Are there some frameworks/packages in Julia which would come close to that? Or which are aiming to provide this in the future.
- DifferentialEquations.jl (+related packages) is great but my simulation is numerically trivial but complex due to a list of biological effects (changing parameters etc). That makes DifferentialEquations.jl unattractive for my case. (Maybe that would change if some domain specific packages are build on top).
- Agents.jl is cool, but like every interface, I find it challenging to fit my model into it.
Some parts are non-intuitive and I cannot control the numerical algorithms as I want.
- BioJulia is more aimed at DNA related things.
(Anyway, I love those packages, don’t get me wrong!)
What differentiates the projects mentioned in the preprint from existing Julia packages seems to be a strong history of implemented and non-trivial models and a very extendable framework to include all kinds of crazy biological effects.