Linear Modelling In Systems Biology

[HenriSpoor]

Hello Guys,

I'm a student who is trying to major in systems biology. My project aims to study how uncertainties propagate through a linear system of differential equations. I've built up my scripts that answer this (one is a monte-carlo style method and the derives differentials for the moments and then infers their maximum entropy distributions). Unfortunately, I can't find a published model (or any model for that matter) to test my scripts on... It has to be linear because non-linear uncertainty propagation is still an open problem and a bit too challenging for a bachelor thesis.

Does anybody know of a compartmental linear model that describes a cellular function ?

Thanks so much guys !

[studiot]

There is some discussion of this subject, plus a few examples to test your algothirms on in

Elementary Numerical Analysis

Conte and de Boor

Page 398ff

 

Numerical methods for Differential Equations

Ortega and Poole

Page 84 to 118

 

But I have not come across any biological applications.

Edited May 23, 2019 by studiot

[CharonY]

There is a large body of literature for a variety of cellular aspects. You may want to check out books on  Biochemcial Systems Theory.  Often , the nonlinear aspects are captured suffciently using ordinary differential equations or at least approximated with power-law relationships. There are also non-dynamic approaches, of which constraint-based ones are particularly popular.

If you want to find a particular one, I suggest to look into carbon metabolism and especially glycolysis, for which many models have been established (predominantly for model organisms such as yeast and E. coli).