Non-zero flux through certain tasks?

[nnursimulu]

Dear developers,

First of all, happy new year! I was looking at getting flux distributions for some of the tasks that you have. For instance, arginine degradation and PAP degradation. While running parsimonious FBA, I get a trivial zero flux distribution for these tasks. I have attempted to force the lower bound to 1 to no avail (infeasible problem). Would you have any guidance on how to get non-zero flux through these tasks?

I look forward to hearing from you!

[JonathanRob]

Hi @nnursimulu, and Happy New Year!

Interesting; when I look at these tasks in the full task list, I noticed that they do not have input or output lower/upper bounds defined in a way that requires them to carry any flux.

For example, PAP degradation specifies the input and output metabolites involved in the task, but there are no bounds set, meaning that this task could in theory be satisfied with a null flux distribution. So really all it's testing is whether the metabolites are present in the model. I could be wrong, but that is my interpretation.

In our previous work, this full task list was not used as extensively as some of the others (such as the essential task list), so it's possible this issue never surfaced.

If my understanding is correct, then maybe the model cannot actually perform these tasks. And if these are tasks that should be possible, then I recommend identifying and correcting the cause of the failure (incorrect bounds, missing reaction(s)/metabolite(s), etc.), and then correcting the task definition in the task list to force flux through it (for example by setting the input(s) LB to 1, or the output(s) LB to 1).

[nnursimulu]

Hi @JonathanRob,

Thank you for clarifying! I will try what you suggested.

All the best!