gap filling and model validation

Rodrigo Colpo

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Sep 29, 2017, 2:07:35 PM9/29/17

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Hi all,

I'm new Cobra user and just finished to read the introductory tutorials.
I created a model on KBase that I would like to validate on different carbon sources, but some of them don't exist in the model yet. So I assume that I must add an exchange reaction for my specific media, for example as:

modelNew = addExchangeRxn(model, {'EX_cpd12375_e0'}, -1000, 1000)

But I receive the error message bellow that I don't quite understand:

Subscript indices must either be real positive integers or logicals.
Error in addExchangeRxn (line 36)
duplicate = find(sum(newModel.S ~= 0, 1) == 1 & any(newModel.S == -1, 1) & any(newModel.S(metOrd,:), 1));

Somehow I have the felling that just adding an exchange reaction name and bounds would not be enough to represent a new media, once I didn't created the links between the exchange reaction and the cellular media, or didn't defined which already existing reactions are directly linked with this exchange reaction. Sorry if my guess is inaccurate.

Once the exchange reactions are created I would like to gapfill the model (I already know that the model don't grow on many medias where it should grow). On COBRApy the gapfill function can suggest more than a single set of gapfilling reactions, and I can't find any function on COBRA Toolbox that give me more than one gapfilling solution. Is there other gapfilling methods on COBRA Toolbox that I can use, or fastGapFill is the only supported gapfilling method on COBRA Toolbox?

Thank you,
Rodrigo.

Will

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Oct 12, 2017, 2:15:12 PM10/12/17

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GrowthExpMatch is available in the COBRA toolbox, but I have never run it so can't comment on its efficacy. If you want a range of potential gap filling solutions, there are several parameters to tune your FastGapFill results. You can specify relative weights with which each type of reaction (enzymatic/transport/exchange) is considered, which could give you a range of possible solutions, depending on your system. These weights are currently hardwired into the code, but can be changed if required.

Ronan M.T. Fleming

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Oct 19, 2017, 11:47:30 PM10/19/17

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Hi Rodrigo,

modelNew = addExchangeRxn(model, {'EX_cpd12375_e0'}, -1000, 1000)

EX_cpd12375_e0 looks like the name of a reaction rather than a metabolite.