I'm making a project about modeling of nannochloropsis metabolism. My model is in the refinement stage. However, it is not running in the FBA test. Then i found there are 87 reactions that did not run. But the reactant/metabolites for those reactions to run are there in the model.

Is there any one know what is the possible reason for this, and how to solve this problem?

Really looking forward to see your answer.



closed as unclear what you're asking by AliceD, March Ho, James, fileunderwater, Amory Nov 3 '15 at 14:20

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  • $\begingroup$ I'm not exactly sure what you're asking I'm afraid. Could you provide some more information? $\endgroup$ – James Oct 29 '15 at 1:02
  • $\begingroup$ Hi Good Gravy, it is about the result of FBA optimizeCbModel when i apply for my metabolic model. it gives f=0, no flux through my model. I think the problem is what @ Roland said. $\endgroup$ – Nhung Pham Oct 29 '15 at 10:22

It is common that reactions in stoichiometric models cannot carry flux because there is a "dead end" metabolite somewhere. The problem may not be in the immediate reactants / products, but can be several steps away, and is not always easy to find.

If you have a network visualization tool, one option is to highlight all reactions that cannot carry flux; often this reveals an entire blocked pathway ending in the isolated metabolites.

A more systematic method is to examine the dual solution of the linear program for maximizing flux through a blocked reaction; this shows the active constraints, which are precisely the metabolites that are lacking for the blocked reaction to be able to run.

  • $\begingroup$ Hi Roland, Thanks for your answer. Do you know which visualization tool that i can use in this case? I'm trying to make with cytoscape but it is quite a bit messy for me. $\endgroup$ – Nhung Pham Oct 29 '15 at 10:27
  • $\begingroup$ Cytoscape should work well, provided you have a graph layout you can just export the graph with node labels reflecting blocked reactions. If you don't have a graph layout it's much more work --- this is not trivial to do automatically, I have always done manual layout. The LP dual method might be easier. $\endgroup$ – Roland Oct 29 '15 at 16:17

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