I would like to simulate a biological pathway in Matlab, Mathematica or Python. To study the response of the pathway using Control Theory. Is there a standard way to simulate pathways by using differential equations or any other formalism.

For example I would like to try to simulate this KEGG pathway map. Is there something more recent than this work from 2005?

For example to simulate Petri networks?

  • $\begingroup$ What do you want to simulate, the concentration of the metabolites through time? Do you have initial concentrations or do you want to study the effect of a condition (drug, variant, food,...) in a pathway? What kind of data do you have? $\endgroup$ – llrs Jan 29 '18 at 7:54
  • $\begingroup$ At the end of the day it's just a system of differential equations, so I'm not sure how helpful some external "pathway simulation" package would be (just use the base matlab or python functions). $\endgroup$ – Devon Ryan Jan 29 '18 at 10:50
  • $\begingroup$ Some equations cannot be solved analytically so they must use numeric approximations that are not trivial. This usually requires specific software on how to deal with the equations. (I am not aware if matlab or python are able to do this, but it is in my opinion a good question). I remember using polymath to solve some differential equations, but it was not used for pathway simulation but for bioreactors $\endgroup$ – llrs Jan 30 '18 at 8:23

In matlab this can be done using the SimBiology toolbox.
In mathematica this can be done using the SystemModeler.
In python there are multiple packages, e.g. (in no particular order) PySB, Tellurium, PySD

  • $\begingroup$ Is there a tool to translate a pathway from KEGG into a set of ODEs or the input formats of SimBiology or PySB? $\endgroup$ – 0x90 Jan 14 '20 at 22:49
  • $\begingroup$ I think what one can do is to download the KGML of the pathway from KEGG as described here and then to load it using KEGGtranslator and export it to SMBL. PySB and Matlab should be able to load SMBL files. $\endgroup$ – 0x90 Jan 15 '20 at 0:04

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