What toolboxes are useful to run with SimBiology?

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I am learning to use SimBiology to streamline generating model equations for my metabolic network. I have 13C and 14C metabolite labeling data obtained from pulse chase labeling of tobacco plants and am just not sure which toolboxes will be useful for analyzing the pathways within the network. I'm pretty sure I should install the optimization toolbox and ODE/PDE toolboxes but what else should I begin learning how to use within SimBiology? I will use the SimBiology interface to generate the pathways/compartments etc. and then I will convert to MatLab code to populate a script with the model equations. Where do I find guidance on these very tedious tasks to gain a more complete understanding of the Simbiology to MatLab integration? I'm doing my PhD in my 4th year and really want to understand the computational techniques I need to generate useful models to fully utilize all the bench time I've spent gathering data through experimentation. Will someone point me in a direction that I can integrate my knowledge of metabolism with the power of computation in Matlab?!??! Thank you all and have a great day/night!

Accepted Answer

Arthur Goldsipe
Arthur Goldsipe on 23 Jul 2021
I recommend simulating your model within SimBiology (that is, using SimBiology's ODE solvers rather than exporting your equations and solving elsewhere). This is often much faster and easier to intepret. So I personally don't see a need to use the PDE Toolbox.
In terms of what other products might be useful, the others I most commonly use are Optimization Toolbox, Global Optimization Toolbox, Statistics and Machine Learning Toolbox, and Parallel Computing Toolbox. I use the Parallel Computing Toolbox to do simulations in parallel, which is especially helpful when trying to paramererize a model. And the other toolboxes I mentioned offer useful methods for doing that parameterization.
For more information on using SimBiology, take a look at the "Get Started" section on this page.

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