Closed mfcesur closed 3 years ago
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I assume that the template model used for gap-filling is the same as the one used to generate the draft model?
What happens if you solve balancedModel
before removing duplicate reactions?As you highlighted, the problem was related to the removed reactions. I manually checked these reactions and solved the problem. Thank you so much for your prompt feedback.
Best Regards
Dear Sir/Madam,
I have reconstructed a genome-scale metabolic network model using an orthology-based approach. However, "cofactors and vitamins" in the biomass equation could not be produced. Therefore, I am trying gap-filling to add the lacking reactions.
To this aim, I defined biomass formation reaction as the objective function for both template and draft models. To allow the addition of growth-related reactions via fillGaps function, I set the lower bound of the biomass formation reaction in draft model to 1e-4. Then, I removed "genes" and "rxnGeneMat" fields from the template model. After performing gap-filling, I removed duplicate reactions using checkDuplicateRxn function. Despite the addition of several reactions via fillGaps, there is no biomass formation even after gap-filling. I used the following syntax: [newConnected, cannotConnect, addedRxns, balancedModel, exitFlag] = fillGaps(dmelGEM1, human_model, true, true, false, []); dmelGEM1: draft model and human_model: template model
I would greatly appreciate if you could provide your comments or suggestions. Thank you so much for your time and consideration.
Best Regards, Müberra