Error in BacArena after loading model generated after gapfilling with LB media about gapseq HOT 6 CLOSED

actually this is a warning and not an error, isn't it :D ?!

The point in BacArena is that it is not clear whether the lower bounds are set as default diet or maximum uptake rates.
For example, a value of -10 in the glucose exchange EX_cpd00027_e0 could be due to the diet or due to the transporter kinetics.
The diet constraints are given by the environment in BacArena (addSubs()) but if there should be any limit of the uptake rates this would overrule the environmental diet constraints.

When adding a model in BacArena, this could not be determined automatically.
This is why a warning is printed but it is not an error!

If you do not have transporter uptake rates set (as it is the case for gapseq models), then it is recommended to use setAllExInf=TRUE when creating the organism in BacArena. In this case, only environmental diet constraints are used.

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Thanks, Yupp that was warning, using setAllExInf=TRUE eliminates warning.
But what exactly the Median lower bound values means as changing the gapfill media changes its value and -1006 seems to be most common value.

Also does this not setting of transporter uptake rates by gapseq can lead to any erroneous prediction in uptake and export of metabolites by the bacterial cells in bac arena ? because my study inclines toward predicting the exchange of metabolites between two or more bacteria.

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sure this is a crucial point and that is why the warning is printed.
In the past, quite some models used this transporter uptake limit to define maximum uptake rates and other exchange reactions were unconstrained. We tried to pay attention to this and integrated maximum uptake rates as default behavior in bacarena.
But I agree that from a gapseq perspective, this makes things a bit complicate.

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So is there way to optimize this uptake rates and metabolite transport fluxes (either in sybil or in cobratoolbox) so that we can accurately predict the exchange of metabolites between two bacteria ? Can exchange of molecules which are in less concentration like vitamins or siderophores can be predicted , because I observe that mostly high concentration moelcule like acetate and formate are reported to be exchanged and even I observed it. The paper "Microbial Community Metabolic
Modeling: A Community Data-Driven Network Reconstruction" by Christopher et al , seems to talk about exchange of wide range of metabolites but they have considered the compartmentalized model system.

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This should definitely be possible and was already done with BacArena several times (for example https://doi.org/10.1038/s41396-019-0504-y bacarena was used to model the crossfeeding of sucrose between Ochrobactrum and Pseudomonas).
I talked with Eugen, we changed the default behavior so that exchange reactions are constrained by the medium only (by default).
Please check out the latest BacArena after the commit: euba/BacArena@29620be
Concerning siderophores, I'm not sure whether genome-scale metabolic modeling which often optimized biomass production can correctly predict this correctly.
Does it makes sense to you?

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Thanks, I will check it and if any issue occur I will post it.

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