Biomakespace Forum

Whole cell modelling simulation and verification experiments


(Ciro Santilli) #1

This is likely naive and impractical since I’m a systems software engineer not a biochemist… but here goes:

Is anyone in the community interested in: https://en.wikipedia.org/wiki/Cellular_model and especially full cell models of simple unicellular organisms?

In particular, I’d like to carry out simulations / experiments of the type:

  • in the simulation, you make up the cell genome / initial cell state
  • let the simulation run and get some measurements that can be measured in practice, e.g.: how long until the cell doubles, what is the concentration of certain chemicals on growth medium, etc
  • measure them on the lab, and see if model is good

This will likely require biological knowledge and measure / manipulation methods that haven’t been researched yet, super computers for the model, and full time work to get anywhere, but here goes my naive dream :slight_smile:

If you have any such interesting cell simulations running on your computer, or open source software that actually works and is easy to get started with, let me know.


(Scott Smith) #2

Hey,

Can you suggest any papers I should read to get an idea of the kinds of equation system being used in these simulations?

In case they are using ODEs, I think your best bet would be something like Octave (https://octave.org/doc/v4.0.3/Ordinary-Differential-Equations.html), although it turns out Python (Scipy) also has some tools for solving ODEs (https://apmonitor.com/pdc/index.php/Main/SolveDifferentialEquations).

I also found a Python/C++ based open source project for solving PDEs that looks pretty easy to use called FEniCS: https://fenicsproject.org/ . Definitely looks like you need some background in mathematics/variational calculus! Haven’t used it myself before, but I might have a play with it if I can find some time.

Let me know what you think!

Many Thanks
Scott Smith


(Ciro Santilli) #3

Just to clarify, I know nothing about the subject yet. :slight_smile:

I’m hoping some bio person here can point to a github repo that model the cells and just work.

But my guess is that there is nothing besides what is already mentioned at: https://en.wikipedia.org/wiki/Cellular_model , and I tried all of them and none just worked.

Hopefully someone will prove my guess wrong :wink:


(Jenny Molloy) #4

Have you had a look at CellModeller?
http://haselofflab.github.io/CellModeller/
There is also a google group as well as the github repo.

This one has been designed to integrate models of cellular biophysics, gene regulation and intercellular signalling. It also makes things look pretty and apparently someone has simulated nutrient fields (Beatles soundtrack probably optional).